Partial Root-Zone Drying of Olive (Olea europaea var. 'Chetoui') Induces Reduced Yield under Field Conditions

PubMed Central

Dbara, Soumaya; Haworth, Matthew; Emiliani, Giovani; Ben Mimoun, Mehdi; Gómez-Cadenas, Aurelio; Centritto, Mauro

2016-01-01

The productivity of olive trees in arid and semi-arid environments is closely linked to irrigation. It is necessary to improve the efficiency of irrigation techniques to optimise the amount of olive fruit produced in relation to the volume of water used. Partial root-zone drying (PRD) is a water saving irrigation technique that theoretically allows the production of a root-to-shoot signal that modifies the physiology of the above-ground parts of the plant; specifically reducing stomatal conductance (gs) and improving water use efficiency (WUE). Partial root-zone drying has been successfully applied under field conditions to woody and non-woody crops; yet the few previous trials with olive trees have produced contrasting results. Thirty year-old olive trees (Olea europaea ‘var. Chetoui’) in a Tunisian grove were exposed to four treatments from May to October for three-years: ‘control’ plants received 100% of the potential evapotranspirative demand (ETc) applied to the whole root-zone; ‘PRD100’ were supplied with an identical volume of water to the control plants alternated between halves of the root-zone every ten-days; ‘PRD50’ were given 50% of ETc to half of the root-system, and; ‘rain-fed’ plants received no supplementary irrigation. Allowing part of the root-zone to dry resulted in reduced vegetative growth and lower yield: PRD100 decreased yield by ~47% during productive years. During the less productive years of the alternate bearing cycle, irrigation had no effect on yield; this suggests that withholding of water during ‘off-years’ may enhance the effectiveness of irrigation over a two-year cycle. The amount and quality of oil within the olive fruit was unaffected by the irrigation treatment. Photosynthesis declined in the PRD50 and rain-fed trees due to greater diffusive limitations and reduced biochemical uptake of CO2. Stomatal conductance and the foliar concentration of abscisic acid (ABA) were not altered by PRD100 irrigation

Partial Root-Zone Drying of Olive (Olea europaea var. 'Chetoui') Induces Reduced Yield under Field Conditions.

PubMed

Dbara, Soumaya; Haworth, Matthew; Emiliani, Giovani; Ben Mimoun, Mehdi; Gómez-Cadenas, Aurelio; Centritto, Mauro

2016-01-01

The productivity of olive trees in arid and semi-arid environments is closely linked to irrigation. It is necessary to improve the efficiency of irrigation techniques to optimise the amount of olive fruit produced in relation to the volume of water used. Partial root-zone drying (PRD) is a water saving irrigation technique that theoretically allows the production of a root-to-shoot signal that modifies the physiology of the above-ground parts of the plant; specifically reducing stomatal conductance (gs) and improving water use efficiency (WUE). Partial root-zone drying has been successfully applied under field conditions to woody and non-woody crops; yet the few previous trials with olive trees have produced contrasting results. Thirty year-old olive trees (Olea europaea 'var. Chetoui') in a Tunisian grove were exposed to four treatments from May to October for three-years: 'control' plants received 100% of the potential evapotranspirative demand (ETc) applied to the whole root-zone; 'PRD100' were supplied with an identical volume of water to the control plants alternated between halves of the root-zone every ten-days; 'PRD50' were given 50% of ETc to half of the root-system, and; 'rain-fed' plants received no supplementary irrigation. Allowing part of the root-zone to dry resulted in reduced vegetative growth and lower yield: PRD100 decreased yield by ~47% during productive years. During the less productive years of the alternate bearing cycle, irrigation had no effect on yield; this suggests that withholding of water during 'off-years' may enhance the effectiveness of irrigation over a two-year cycle. The amount and quality of oil within the olive fruit was unaffected by the irrigation treatment. Photosynthesis declined in the PRD50 and rain-fed trees due to greater diffusive limitations and reduced biochemical uptake of CO2. Stomatal conductance and the foliar concentration of abscisic acid (ABA) were not altered by PRD100 irrigation, which may indicate the

Immunological Evidence for the Existence of a Carrier Protein for Sucrose Transport in Tonoplast Vesicles from Red Beet (Beta vulgaris L.) Root Storage Tissue.

PubMed Central

Getz, H. P.; Grosclaude, J.; Kurkdjian, A.; Lelievre, F.; Maretzki, A.; Guern, J.

1993-01-01

Monoclonal antibodies were raised in mice against a highly purified tonoplast fraction from isolated red beet (Beta vulgaris L. ssp. conditiva) root vacuoles. Positive hybridoma clones and sub-clones were identified by prescreening using an enzyme-linked immunosorbent assay (ELISA) and by postscreening using a functional assay. This functional assay consisted of testing the impact of hybridoma supernatants and antibody-containing ascites fluids on basal and ATP-stimulated sugar uptake in vacuoles, isolated from protoplasts, as well as in tonoplast vesicles, prepared from tissue homogenates of red beet roots. Antibodies from four clones were particularly positive in ELISAs and they inhibited sucrose uptake significantly. These antibodies were specific inhibitors of sucrose transport, but they exhibited relatively low membrane and species specificity since uptake into red beet root protoplasts and sugarcane tonoplast vesicles was inhibited as well. Fast protein liquid chromatography assisted size exclusion chromatography on Superose 6 columns yielded two major peaks in the 55 to 65-kD regions and in the 110- to 130-kD regions of solubilized proteins from red beet root tonoplasts, which reacted positively in immunoglobulin-M(IgM)-specific ELISAs with anti-sugarcane tonoplast monoclonal IgM antibodies. Only reconstituted proteoliposomes containing polypeptides from the 55- to 65-kD band took up [14C]-sucrose with linear rates for 2 min, suggesting that this fraction contains the tonoplast sucrose carrier. PMID:12231863

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.

Soil type affects Pinus ponderosa var. scopulorum (Pinaceae) seedling growth in simulated drought experiments1

PubMed Central

Lindsey, Alexander J.; Kilgore, Jason S.

2013-01-01

• Premise of the study: Effects of drought stress and media type interactions on growth of Pinus ponderosa var. scopulorum germinants were investigated. • Methods and Results: Soil properties and growth responses under drought were compared across four growth media types: two native soils (dolomitic limestone and granite), a soil-less industry standard conifer medium, and a custom-mixed conifer medium. After 35 d of growth, the seedlings under drought stress (reduced watering) produced less shoot and root biomass than watered control seedlings. Organic media led to decreased root biomass, but increased root length and shoot biomass relative to the mineral soils. • Conclusions: Media type affected root-to-shoot biomass partitioning of P. ponderosa var. scopulorum, which may influence net photosynthetic rates, growth, and long-term seedling survival. Further work should examine how specific soil properties like bulk density and organic matter influence biomass allocation in greenhouse studies. PMID:25202578

Effects of exogenous glutathione and cysteine on growth, lead accumulation, and tolerance of Iris lactea var. chinensis.

PubMed

Yuan, Haiyan; Zhang, Yongxia; Huang, Suzhen; Yang, Yongheng; Gu, Chunsun

2015-02-01

Effects of exogenous reduced glutathione (GSH) and cysteine (Cys) on growth, lead (Pb) accumulation, and nonprotein thiol (NPT) contents of Iris lactea var. chinensis under 100 and 500 mg L(-1) Pb stress were studied. Our results showed that 500 mg L(-1) Pb stress caused a dramatical decline in fresh weights, while the reduction of aboveground biomass was alleviated by exogenous GSH and Cys even though keeping higher Pb contents in roots and shoots. Exogenous GSH and Cys could enhance Pb accumulation in the shoots and roots compared with single Pb treatment. The promoting effect of GSH to Pb accumulation was larger than the effect of Cys, and the Pb contents in the shoots and roots treated with 500 mg L(-1) Pb + GSH reached 1,712 and 14,603 mg kg(-1), about 4.19 and 2.78 times of single 500 mg L(-1) Pb treatment, respectively. Microscopic imaging of Pb in roots and leaves showed that higher intensive fluorescence was observed in cell wall of root epidermis, stele, vascular tissues of the roots, and sclerenchyma cells of leaves treated with 500 mg L(-1) Pb + GSH and treated with 500 mg L(-1) Pb + Cys. Exogenous GSH had an apparent promoting effect on root and shoot GSH synthesis, while exogenous Cys reduced the synthesis of cellular GSH in shoot and increased Cys contents. Pb only induced the synthesis of phytochelatin (PC)2 in roots, and the PC2 content declined in GSH- and Cys-treated plant roots. These results suggested that GSH synthesis was a more effective approach to improve Pb accumulation and translocation of I. lactea var. chinensis. Further analysis of protein expression in plants by exogenous GSH and buthionine sulfoximine (BSO) application showed that the proteins regulated by GSH and BSO may constitute various enzymes involved in GSH biosynthesis and play certain roles in Pb accumulation and tolerance of I. lactea var. chinensis.

Studies on black stain root disease in ponderosa pine. pp. 236-240. M. Garbelotto & P. Gonthier (Editors). Proceedings 12th International Conference on Root and Butt Rots of Forest Trees.

Treesearch

W. J. Otrosina; J. T. Kliejunas; S. S. Sung; S. Smith; D. R. Cluck

2008-01-01

Black stain root disease of ponderosa pine, caused by Lepfographium wageneri var. ponderosum (Harrington & Cobb) Harrington & Cobb, is increasing on many eastside pine stands in northeastern California. The disease is spread from tree to tree via root contacts and grafts but new infections are likely vectored by root...

NMR analysis reveals a wealth of metabolites in root-knot nematode resistant roots of Citrullus amarus watermelon plants

USDA-ARS?s Scientific Manuscript database

Citrullus amarus (CA) (previously known as Citrullus lanatus var. citroides) accessions collected in southern Africa are known to have resistance to root-knot nematodes (RKN) and are suitable rootstocks for grafted watermelon. A comparative metabolomics study was performed to identify unique metabol...

RELATING FINE ROOT BIOMASS TO SOIL AND CLIMATE CONDITIONS IN THE PACIFIC NORTHWEST

EPA Science Inventory

The additive contribution of fine root biomass for Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco var. menziesii) and western hemlock (Tsuga heterophylla (Raf.) Sarg.) to the stand average fine root biomass were estimated for eight conifer stands in the Pacific Northwest. Base...

Quantifying coastal erosion rates using anatomical change in exposed tree roots at Porquerolles Island (Var, France).

NASA Astrophysics Data System (ADS)

Morel, Pauline; Corona, Christophe; Lopez-Saez, Jérôme; Rovéra, Georges; Dewez, Thomas; Stoffel, Markus; Berger, Frédéric

2017-04-01

Rocky coasts are the most common type of ocean-land contacts and can be found in all types of morphogenetic environments. Most work on rocky environments focused on the impacts of modern sea level rise on cliff stability derived from sequential surveys, direct measurements or erosional features in anthropogenic structures. Studies mainly focused on rapid erosion so that little is known about erosion rates of the French Mediterranean coastal area. Using anatomical reactions in roots, has been successfully used in various environments in the past to quantify continuous denudation rates, mostly in relation with gullying processes (Vandekerckhove, 2001; Malik, 2008), aerial (or sheet) (Bodoque et al., 2005; Lopez Saez et al., 2011; Lucia et al., 2011), river bank (Malik, 2006; Hitz et al., 2008a; Stoffel et al., 2012), or lake shore (Fantucci, 2007) erosion, but never so far on coastal cliffs environment. This study aims at exploring the potential of dendrogeomorphic approach to quantify multidecadal changes in coastal environments on Porquerolles Island (Var, France). We sampled 56 discs from Pinus halepensis Mill. roots on former alluvial deposits eroded by present day sea level (escarpments of a few meter in height) and on sandy-gravelly cliffs. We were able to dates erosion pulses as well as changes in cliff geometry with annual resolution over 30-40 years showing an average erosion rate of 2.1 cm yr-1. Our results are consistent with those found in the study of Giuliano (2015) on Mediterranean coastal environment. This contribution therefore demonstrates that dendrogeomorphic analyses of roots clearly have significant potential and are a powerful tool for the quantification of multidecadal cliff retreats rates in areas where measurements of past erosion is lacking. References: Bodoque J, Díez-Herrero A, Martín-Duque J, Rubiales J, Godfrey A, Pedraza J, Carrasco R, Sanz M. 2005. Sheet erosion rates determined by using dendrogeomorphological analysis of exposed

[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.

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.

Allelopathy of the invasive plant Bidens frondosa on the seed germination of Geum japonicum var. chinense.

PubMed

Wang, X F; Hassani, D; Cheng, Z W; Wang, C Y; Wu, J

2014-12-12

Five gradient concentrations (0.02, 0.04, 0.06, 0.08, and 0.10 g/mL) of leaching liquors from the roots, stems, and leaves of the invasive plant Bidens frondosa were used as conditioning fluid to examine its influence on seed germination conditions of the native plant Geum japonicum var. chinense in Huangshan. All leaching liquors of organs suppressed the seed germination of Geum japonicum var. chinense and reduced the final germination percentage and rate, and increased the germination inhibition rate, with a bimodal dependence on concentration. The leaching liquor inhibited the seed germination significantly at the concentration of 0.02 g/mL respectively. The seed germination was also inhibited as the concentration reached to 0.04 g/mL and beyond. Hence the allelopathic effects of the organs were significantly enhanced respectively. This phenomenon represented the presence of allelopathy substances in the root, stem and leaf of Bidens frondosa.

Micropropagation of globe artichoke (Cynara cardunculus L. var. scolymus).

PubMed

Iapichino, Giovanni

2013-01-01

The globe artichoke (Cynara cardunculus L. var. scolymus) is a perennial plant cultivated in the Mediterranean region and the Americas for its edible young flower heads. Although vegetative propagation by offshoots or by "ovoli" (underground dormant axillary buds) has been the primary method of propagation, the potential for the diffusion of diseases and the phenotypic variability can be very high. The propagation of this species by axillary shoot proliferation from in vitro-cultured meristems produces systemic pathogen-free plants and a higher multiplication rate as compared to that obtained by conventional agamic multiplication. Axillary shoot proliferation can be induced from excised shoot apices cultured on Murashige and Skoog agar solidified medium supplemented with various concentrations of cytokinins and auxins, depending on genotype. For the production of virus-free plants, meristems, 0.3-0.8 mm long are excised from shoot apices and surface sterilized. The transfer of artichoke microshoots to a medium lacking cytokinins or with low cytokinin concentration is critical for rooting. Adventitious roots develop within 3-5 weeks after transfer to root induction MS medium containing NAA or IAA at various concentrations. However, in vitro rooting frequency rate is dependent on the genotype and the protocol used. Acclimatization of in vitro microshoots having 3-4 roots is successfully accomplished; plantlets develop new roots in ex vitro conditions and continue to grow.

Evaluation of coffee genotypes for root-knot nematode resistance

USDA-ARS?s Scientific Manuscript database

Meloidogyne konaensis causes severe damage to the root systems of Coffea arabica cv. Typica ‘Guatemala’ grown in Kona, Hawaii. Farmers currently employ grafting of the nematode tolerant C. liberica var. dewevrei ‘Fukunaga’ to C. arabica cv. Typica scions. Greenhouse experiments confirmed C. liberi...

Black stain root disease studies on ponderosa pine parameters and disturbance treatments affecting infection and mortality

Treesearch

W.J. Otrosina; J.T. Kliejunas; S. Smith; D.R. Cluck; S.S. Sung; C.D. Cook

2007-01-01

Black stain root disease of ponderosa pine (Pinus ponderosa Doug. Ex Laws.), caused by Leptographium wageneri var. ponderosum (Harrington & Cobb) Harrington & Cobb, is increasing on many eastside Sierra Nevada pine stands in northeastern California. The disease is spread from tree to tree via root...

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.

Volvalerine A, an unprecedented N-containing sesquiterpenoid dimer derivative from Valeriana officinalis var. latifolia.

PubMed

Wang, Peng-Cheng; Ran, Xin-Hui; Luo, Huai-Rong; Ma, Qing-Yun; Zhou, Jun; Hu, Jiang-Miao; Zhao, You-Xing

2016-03-01

Volvalerine A (1), a novel N-containing bisesquiterpenoid derivative with a dihydroisoxazole ring, and its possible biosynthetic precursor, 1-hydroxy-1,11,11-trimethyldecahydrocyclopropane azulene-10-one (2), were isolated from the roots of Valeriana officinalis var. latifolia. Their structures and relative configurations were identified using spectroscopic data and X-ray crystallography. A plausible biosynthetic pathway for 1 is also presented. Copyright © 2016 Elsevier B.V. All rights reserved.

Dispersion of kaolinite by dissolved organic matter from Douglas-fir roots

Treesearch

Philip B. Durgin; Jesse G. Chaney

1984-01-01

The organic constituents of water extracts from Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco var. menziesii) roots that cause kaolinite dispersion were investigated. The dissolved organic matter was fractionated according to molecular size and chemical characteristics into acids, neutrals, and bases of the hydrophilic and hydrophobic groups.

Rhizobium capsici sp. nov., isolated from root tumor of a green bell pepper (Capsicum annuum var. grossum) plant.

PubMed

Lin, Shih-Yao; Hung, Mei-Hua; Hameed, Asif; Liu, You-Cheng; Hsu, Yi-Han; Wen, Cheng-Zhe; Arun, A B; Busse, Hans-Jürgen; Glaeser, Stefanie P; Kämpfer, Peter; Young, Chiu-Chung

2015-03-01

A novel, Gram-staining-negative, rod-shaped, aerobic and motile bacterium, designated strain CC-SKC2(T), was isolated from the root tumor of a green bell pepper (Capsicum annuum var. grossum) plant in Taiwan. Cells were positive for oxidase and catalase activities and exhibited growth at 25-37 °C, pH 4.0-9.0 and tolerated NaCl concentrations up to 4.0 % (w/v). Strain CC-SKC2(T) is able to trigger nodulation in soybean (Glycine max Merr.), but not in Capsicum annuum var. grossum, red bean (Vigna angularis), sesbania (Sesbania roxburghii Merr.) or alfalfa (Medicago varia Martin.). The novel strain shared highest 16S rRNA gene sequence similarity to Rhizobium rhizoryzae KCTC 23652(T) and Rhizobium straminoryzae CC-LY845(T) (both 97.5 %) followed by Rhizobium lemnae L6-16(T) (97.3 %), Rhizobium pseudoryzae KCTC 23294(T) (97.1 %), and Rhizobium paknamense NBRC 109338(T) (97.0 %), whereas other Rhizobium species shared <96.7 % similarity. The DNA-DNA relatedness values of strain CC-SKC2(T) with R. rhizoryzae KCTC 23652(T), R. pseudoryzae KCTC 23294(T) and R. paknamense NBRC 109338(T) were 11.4, 17.2 and 17.0 %, respectively (reciprocal values were 11.1, 28.3 and 24.0 %, respectively). Phylogenetic analysis based on 16S rRNA, atpD and recA genes revealed a distinct taxonomic position attained by strain CC-SKC2(T) with respect to other Rhizobium species. The major fatty acids in strain CC-SKC2(T) were C16:0, C19:0 cyclo ω8c, C14:0 3-OH and/or C16:1 iso I and C18:1 ω7c and/or C18:1 ω6c. The polyamine pattern showed predominance of spermidine and moderate amounts of sym-homospermidine. The predominant quinone system was ubiquinone (Q-10) and the DNA G+C content was 60.5 mol%. On the basis of polyphasic taxonomic evidence presented here, strain CC-SKC2(T) is proposed to represent a novel species within the genus Rhizobium, for which the name Rhizobium capsici sp. nov. is proposed. The type strain is CC-SKC2(T) (=BCRC 80699(T) = JCM 19535(T)).

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.

Allelopathic effects of water extracts ofArtemisia princeps var.orientalis on selected plant species.

PubMed

Kil, B S; Yun, K W

1992-01-01

The allelopathic effects of wormwood plants (Artemisia princeps var.orientalis) and their possible phytotoxicity on receptor species were investigated. The aqueous extracts of mature leaf, stem, and root of wormwood plants caused significant inhibition in germination and decreased seedling elongation of receptor plants, whereas germination of some species was not inhibited by extracts of stems and roots. Dry weight growth was slightly increased at lower concentrations of the extract, whereas it was proportionally inhibited at higher concentrations. The calorie value of the organic matter in receptor plants measured by bomb calorimeter was reduced proportionally to the extract concentration. However, results with extracts of juvenile leaf did not correlate with inhibition or promotion of elongation and dry weight.

Root Uptake of Lipophilic Zinc−Rhamnolipid Complexes

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

Stacey, Samuel P.; McLaughlin, Michael J.; Cakmak, Ismail

This study investigated the formation and plant uptake of lipophilic metal-rhamnolipid complexes. Monorhamnosyl and dirhamnosyl rhamnolipids formed lipophilic complexes with copper (Cu), manganese (Mn), and zinc (Zn). Rhamnolipids significantly increased Zn absorption by Brassica napus var. Pinnacle roots in {sup 65}Zn-spiked ice-cold solutions, compared with ZnSO{sub 4} alone. Therefore, rhamnolipid appeared to facilitate Zn absorption via a nonmetabolically mediated pathway. Synchrotron XRF and XAS showed that Zn was present in roots as Zn-phytate-like compounds when roots were treated with Zn-free solutions, ZnSO{sub 4}, or Zn-EDTA. With rhamnolipid application, Zn was predominantly found in roots as the Zn-rhamnolipid complex. When appliedmore » to a calcareous soil, rhamnolipids increased dry matter production and Zn concentrations in durum (Triticum durum L. cv. Balcali-2000) and bread wheat (Triticum aestivum L. cv. BDME-10) shoots. Rhamnolipids either increased total plant uptake of Zn from the soil or increased Zn translocation by reducing the prevalence of insoluble Zn-phytate-like compounds in roots.« less

First report of root rot of Chicory caused by Phytophthora cryptogea in Chile

USDA-ARS?s Scientific Manuscript database

Chicory (Cichorium intybus L. var sativum Bisch.), a relatively new high value crop in Chile, was introduced for commercial production of inulin. Inulins are polysaccharides extracted from chicory tap roots that are used in processed foods due to their beneficial gastrointestinal properties. Approxi...

Fusarium species associated with rhizosphere soil and diseased roots of eastern white pine seedlings and associated nursery soil

Treesearch

Cynthia M. Ocamb; Jennifer Juzwik

1995-01-01

Fusarium species isolated from necrotic roots of eastern white pine (Pinus strobus) seedlings in two nurseries included F. acuminatum, F. equiseti, F. oxysporum, F. oxysporum var. redolens, F. proliferatum, F....

Efficacy of a Simple Formulation Composed of Nematode-Trapping Fungi and Bidens pilosa var. radiata Scherff Aqueous Extracts (BPE) for Controlling the Southern Root-Knot Nematode

PubMed Central

Ajitomi, Atsushi; Taba, Satoshi; Ajitomi, Yoshino; Kinjo, Misa; Sekine, Ken-taro

2018-01-01

We tested a formulation composed of a mixture of Bidens pilosa var. radiata extract (BPE) and nematode-trapping fungi for its effects on Meloidogyne incognita. In earlier evaluations of the effects of plant extracts on the hyphal growth of 5 species of nematode-trapping fungi with different capture organs (traps), the growth of all species was slightly inhibited. However, an investigation on the number of capture organs and nematode-trapping rates revealed that Arthrobotrys dactyloides formed significantly more rings and nematode traps than those of the control. An evaluation of simple mixed formulations prepared using sodium alginate showed that nematodes were captured with all formulations tested. The simple mixed formulation showed a particularly high capture rate. Furthermore, in a pot test, although the effects of a single formulation made from the fungus or plant extract were acceptable, the efficacy of the simple mixed formulation against M. incognita root-knot formation was particularly high. PMID:29311429

The GIST Model for Selection and Modification of Scientific Research for the College Teaching Laboratory Based on Root Competition Investigations

ERIC Educational Resources Information Center

Elliott, Shannon Snyder

2007-01-01

The purpose of this study is to first develop an 8-week college teaching module based on root competition literature. The split-root technique is adapted for the teaching laboratory, and the Sugar Ann English pea (Pisum sativum var. Sugar Ann English) is selected as the species of interest prior to designing experiments, either original or…

An Efficient Method for Adventitious Root Induction from Stem Segments of Brassica Species

PubMed Central

Srikanth, Sandhya; Choong, Tsui Wei; Yan, An; He, Jie; Chen, Zhong

2016-01-01

Plant propagation via in vitro culture is a very laborious and time-consuming process. The growth cycle of some of the crop species is slow even in the field and the consistent commercial production is hard to maintain. Enhanced methods of reduced cost, materials and labor significantly impact the research and commercial production of field crops. In our studies, stem-segment explants of Brassica species were found to generate adventitious roots (AR) in aeroponic systems in less than a week. As such, the efficiency of rooting from stem explants of six cultivar varieties of Brassica spp was tested without using any plant hormones. New roots and shoots were developed from Brassica alboglabra (Kai Lan), B. oleracea var. acephala (purple kale), B. rapa L. ssp. chinensis L (Pai Tsai, Nai Bai C, and Nai Bai T) explants after 3 to 5 days of growing under 20 ± 2°C cool root zone temperature (C-RZT) and 4 to 7 days in 30 ± 2°C ambient root zone temperature (A-RZT). At the base of cut end, anticlinal and periclinal divisions of the cambial cells resulted in secondary xylem toward pith and secondary phloem toward cortex. The continuing mitotic activity of phloem parenchyma cells led to a ring of conspicuous white callus. Root initials formed from the callus which in turn developed into ARs. However, B. rapa var. nipposinica (Mizuna) explants were only able to root in C-RZT. All rooted explants were able to develop into whole plants, with higher biomass obtained from plants that grown in C-RZT. Moreover, explants from both RZTs produced higher biomass than plants grown from seeds (control plants). Rooting efficiency was affected by RZTs and explant cuttings of donor plants. Photosynthetic CO2 assimilation rate (Asat) and stomatal conductance (gssat) were significantly differentiated between plants derived from seeds and explants at both RZTs. All plants in A-RZT had highest transpiration rates. PMID:27446170

Volvalerelactones A and B, two new sesquiterpenoid lactones with an unprecedented skeleton from Valeriana officinalis var. latifolia.

PubMed

Wang, Peng-Cheng; Ran, Xin-Hui; Luo, Huai-Rong; Hu, Jiang-Miao; Chen, Rui; Ma, Qing-Yun; Dai, Hao-Fu; Liu, Yu-Qing; Xie, Ming-Jin; Zhou, Jun; Zhao, You-Xing

2011-06-17

Volvalerelactones A and B (1 and 2), two new sesquiterpenoid lactones with an unprecedented 3/7/6 tricyclic ring system, were isolated from the roots of Valeriana officinalis var. latifolia. Their structures and relative configurations were elucidated by spectroscopic data and single-crystal X-ray diffraction crystallography, and the absolute configuration was assigned by computational methods. The possible biosynthetic pathways of 1 and 2 were also proposed. © 2011 American Chemical Society

Determination of five flavonoids in different parts of Fordia cauliflora by ultra performance liquid chromatography/triple-quadrupole mass spectrometry and chemical comparison with the root of Millettia pulchra var. laxior

PubMed Central

2013-01-01

Background The root of Fordia cauliflora Hemsl (FC) has long been used in southern China for the treatment of rheumatism, bruises, dementia in children, and valetudinarianism. However, sometimes it is mixed with other parts. And it has always been confused with the root of Millettia pulchra (Benth.) Kurz var. laxior (Dunn) Z. Wei (MP) by the local people. The chemical differences between the two ethnic drugs are not clear until now. The aim of this study is to develop a precise and accurate method to characterize and quantify multiple chemical components of FC, which is helpful for the quality evaluation and identification of FC. Results A method coupling ultra performance liquid chromatography (UPLC) with triple-quadrupole mass spectrometry (QqQ-MS) was first developed for simultaneous determination of five flavonoids in different parts of FC and the root of MP, based on a UPLC-diode array detection (DAD) fingerprint method. All calibration curves showed good linearity (R2>0.99) within test ranges. The overall LOD and LOQ were lower than 2.5 ng/mL and 5.0 ng/mL, respectively. The RSDs for intra- and inter-day of five analytes were less than 2.83% and 3.04%, respectively. Recovery studies for the quantified compounds were found to be within the range 93.6-99.8% with RSD less than 5.73%. The results suggest that the root, traditionally used medicinal part, yields the highest flavanoid content in FC. Pachycarin A, 3′,4′-dimethoxy(2′′,3′′:7,8) furanoflavone, karanjachromene and isoderricin A can be used to differentiate between FC and MP samples. Conclusions The present method is specific, precise and reliable, and is suitable for characterizing and quantifying multiple chemical components of FC. PMID:23870070

Effects of light on protein patterns in gravitropically stimulated root caps of corn

NASA Technical Reports Server (NTRS)

Feldman, L. J.; Gildow, V.

1984-01-01

In certain cultivars of corn (Zea mays var. Merit), light stimulates gravitropic bending of the root by influencing events in the root cap. In this paper, we report on changes in root cap proteins which occur as a result of the light treatment and single out specific proteins as potentially having a role in mediating the gravitropic response. For this work, we have used root caps maintained aseptically in culture media supplemented with auxin. If auxin is deleted from the culture medium, the protein profiles observed following illumination differ from that seen in caps provided light while in auxin-supplemented media. We also report that several of the proteins for which synthesis is stimulated by light appear to turn over rapidly, usually within 0.5 hour of formation.

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.

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

Four New Flavonoids with α-Glucosidase Inhibitory Activities from Morus alba var. tatarica.

PubMed

Zhang, Ya-Long; Luo, Jian-Guang; Wan, Chuan-Xing; Zhou, Zhong-Bo; Kong, Ling-Yi

2015-11-01

Four new flavonoids, mortatarins A-D (1-4, resp.), along with eight known flavonoids (5-12) were isolated from the root bark of Morus alba var. tatarica. Their structures were established on the basis of spectroscopic data analysis, and the absolute configuration of 4 was determined by analysis of its CD spectrum. All isolates were tested for inhibitory activities against α-glucosidase. Compounds 4, 7, and 8 exhibited a significant degree of inhibition with IC50 values of 5.0 ± 0.3, 7.5 ± 0.5, and 5.9 ± 0.2 μM, respectively. Copyright © 2015 Verlag Helvetica Chimica Acta AG, Zürich.

Chemical Variability and Biological Activities of Brassica rapa var. rapifera Parts Essential Oils Depending on Geographic Variation and Extraction Technique.

PubMed

Saka, Boualem; Djouahri, Abderrahmane; Djerrad, Zineb; Terfi, Souhila; Aberrane, Sihem; Sabaou, Nasserdine; Baaliouamer, Aoumeur; Boudarene, Lynda

2017-06-01

In the present work, the Brassica rapa var. rapifera parts essential oils and their antioxidant and antimicrobial activities were investigated for the first time depending on geographic origin and extraction technique. Gas-chromatography (GC) and GC/mass spectrometry (MS) analyses showed several constituents, including alcohols, aldehydes, esters, ketones, norisoprenoids, terpenic, nitrogen and sulphur compounds, totalizing 38 and 41 compounds in leaves and root essential oils, respectively. Nitrogen compounds were the main volatiles in leaves essential oils and sulphur compounds were the main volatiles in root essential oils. Qualitative and quantitative differences were found among B. rapa var. rapifera parts essential oils collected from different locations and extracted by hydrodistillation and microwave-assisted hydrodistillation techniques. Furthermore, our findings showed a high variability for both antioxidant and antimicrobial activities. The highlighted variability reflects the high impact of plant part, geographic variation and extraction technique on chemical composition and biological activities, which led to conclude that we should select essential oils to be investigated carefully depending on these factors, in order to isolate the bioactive components or to have the best quality of essential oil in terms of biological activities and preventive effects in food. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

Acetylcholine causes rooting in leaf explants of in vitro raised tomato (Lycopersicon esculentum Miller) seedlings.

PubMed

Bamel, Kiran; Gupta, Shrish Chandra; Gupta, Rajendra

2007-05-30

The animal neurotransmitter acetylcholine (ACh) induces rooting and promotes secondary root formation in leaf explants of tomato (Lycopersicon esculentum Miller var. Pusa Ruby), cultured in vitro on Murashige and Skoog's medium. The roots originate from the midrib of leaf explants and resemble taproot. ACh at 10(-5) M was found to be the optimum over a wide range of effective concentrations between 10(-7) and 10(-3) M. The breakdown products, choline and acetate were ineffective even at 10(-3) M concentration. ACh appears to have a natural role in tomato rhizogenesis because exogenous application of neostigmine, an inhibitor of ACh hydrolysis, could mimic the effect of ACh. Neostigmine, if applied in combination with ACh, potentiated the ACh effect.

Evaluation of allelopathic, decomposition and cytogenetic activities of Jasminum officinale L. f. var. grandiflorum (L.) Kob. on bioassay plants.

PubMed

Teerarak, Montinee; Laosinwattana, Chamroon; Charoenying, Patchanee

2010-07-01

Methanolic extracts prepared from dried leaves of Jasminum officinale f. var. grandiflorum (L.) Kob. (Spanish jasmine) inhibited seed germination and stunted both root and shoot length of the weeds Echinochloa crus-galli (L.) Beauv. and Phaseolus lathyroides L. The main active compound was isolated and determined by spectral data as a secoiridoid glucoside named oleuropein. In addition, a decrease in allelopathic efficacy appeared as the decomposition periods increased. The mitotic index in treated onion root tips decreased with increasing concentrations of the extracts and longer periods of treatment. Likewise, the mitotic phase index was altered in onion incubated with crude extract. Furthermore, crude extract produced mitotic abnormalities resulting from its action on chromatin organization and mitotic spindle. Copyright (c)2010 Elsevier Ltd. All rights reserved.

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.

Biological control of wheat root diseases by the CLP-producing strain Pseudomonas fluorescens HC1-07.

PubMed

Yang, Ming-Ming; Wen, Shan-Shan; Mavrodi, Dmitri V; Mavrodi, Olga V; von Wettstein, Diter; Thomashow, Linda S; Guo, Jian-Hua; Weller, David M

2014-03-01

Pseudomonas fluorescens HC1-07, previously isolated from the phyllosphere of wheat grown in Hebei province, China, suppresses the soilborne disease of wheat take-all, caused by Gaeumannomyces graminis var. tritici. We report here that strain HC1-07 also suppresses Rhizoctonia root rot of wheat caused by Rhizoctonia solani AG-8. Strain HC1-07 produced a cyclic lipopeptide (CLP) with a molecular weight of 1,126.42 based on analysis by electrospray ionization mass spectrometry. Extracted CLP inhibited the growth of G. graminis var. tritici and R. solani in vitro. To determine the role of this CLP in biological control, plasposon mutagenesis was used to generate two nonproducing mutants, HC1-07viscB and HC1-07prtR2. Analysis of regions flanking plasposon insertions in HC1-07prtR2 and HC1-07viscB revealed that the inactivated genes were similar to prtR and viscB, respectively, of the well-described biocontrol strain P. fluorescens SBW25 that produces the CLP viscosin. Both genes in HC1-07 were required for the production of the viscosin-like CLP. The two mutants were less inhibitory to G. graminis var. tritici and R. solani in vitro and reduced in ability to suppress take-all. HC1-07viscB but not HC-07prtR2 was reduced in ability to suppress Rhizoctonia root rot. In addition to CLP production, prtR also played a role in protease production.

Chromosome Doubling of Microspore-Derived Plants from Cabbage (Brassica oleracea var. capitata L.) and Broccoli (Brassica oleracea var. italica L.)

PubMed Central

Yuan, Suxia; Su, Yanbin; Liu, Yumei; Li, Zhansheng; Fang, Zhiyuan; Yang, Limei; Zhuang, Mu; Zhang, Yangyong; Lv, Honghao; Sun, Peitian

2015-01-01

Chromosome doubling of microspore-derived plants is an important factor in the practical application of microspore culture technology because breeding programs require a large number of genetically stable, homozygous doubled haploid plants with a high level of fertility. In the present paper, 29 populations of microspore-derived plantlets from cabbage (Brassica oleracea var. capitata) and broccoli (Brassica oleracea var. italica) were used to study the ploidy level and spontaneous chromosome doubling of these populations, the artificial chromosome doubling induced by colchicine, and the influence of tissue culture duration on the chromosomal ploidy of the microspore-derived regenerants. Spontaneous chromosome doubling occurred randomly and was genotype dependent. In the plant populations derived from microspores, there were haploids, diploids, and even a low frequency of polyploids and mixed-ploidy plantlets. The total spontaneous doubling in the 14 cabbage populations ranged from 0 to 76.9%, compared with 52.2 to 100% in the 15 broccoli populations. To improve the rate of chromosome doubling, an efficient and reliable artificial chromosome doubling protocol (i.e., the immersion of haploid plantlet roots in a colchicine solution) was developed for cabbage and broccoli microspore-derived haploids. The optimal chromosome doubling of the haploids was obtained with a solution of 0.2% colchicine for 9–12 h or 0.4% colchicine for 3–9 h for cabbage and 0.05% colchicine for 6–12 h for broccoli. This protocol produced chromosome doubling in over 50% of the haploid genotypes for most of the populations derived from cabbage and broccoli. Notably, after 1 or more years in tissue culture, the chromosomes of the haploids were doubled, and most of the haploids turned into doubled haploid or mixed-ploidy plants. This is the first report indicating that tissue culture duration can change the chromosomal ploidy of microspore-derived regenerants. PMID:26734028

Chromosome Doubling of Microspore-Derived Plants from Cabbage (Brassica oleracea var. capitata L.) and Broccoli (Brassica oleracea var. italica L.).

PubMed

Yuan, Suxia; Su, Yanbin; Liu, Yumei; Li, Zhansheng; Fang, Zhiyuan; Yang, Limei; Zhuang, Mu; Zhang, Yangyong; Lv, Honghao; Sun, Peitian

2015-01-01

Chromosome doubling of microspore-derived plants is an important factor in the practical application of microspore culture technology because breeding programs require a large number of genetically stable, homozygous doubled haploid plants with a high level of fertility. In the present paper, 29 populations of microspore-derived plantlets from cabbage (Brassica oleracea var. capitata) and broccoli (Brassica oleracea var. italica) were used to study the ploidy level and spontaneous chromosome doubling of these populations, the artificial chromosome doubling induced by colchicine, and the influence of tissue culture duration on the chromosomal ploidy of the microspore-derived regenerants. Spontaneous chromosome doubling occurred randomly and was genotype dependent. In the plant populations derived from microspores, there were haploids, diploids, and even a low frequency of polyploids and mixed-ploidy plantlets. The total spontaneous doubling in the 14 cabbage populations ranged from 0 to 76.9%, compared with 52.2 to 100% in the 15 broccoli populations. To improve the rate of chromosome doubling, an efficient and reliable artificial chromosome doubling protocol (i.e., the immersion of haploid plantlet roots in a colchicine solution) was developed for cabbage and broccoli microspore-derived haploids. The optimal chromosome doubling of the haploids was obtained with a solution of 0.2% colchicine for 9-12 h or 0.4% colchicine for 3-9 h for cabbage and 0.05% colchicine for 6-12 h for broccoli. This protocol produced chromosome doubling in over 50% of the haploid genotypes for most of the populations derived from cabbage and broccoli. Notably, after 1 or more years in tissue culture, the chromosomes of the haploids were doubled, and most of the haploids turned into doubled haploid or mixed-ploidy plants. This is the first report indicating that tissue culture duration can change the chromosomal ploidy of microspore-derived regenerants.

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

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.

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

Foliar application of pyraclostrobin fungicide enhances the growth, rhizobial-nodule formation and nitrogenase activity in soybean (var. JS-335).

PubMed

Joshi, Juhie; Sharma, Sonika; Guruprasad, K N

2014-09-01

A field study was conducted to investigate the impact of the fungicide pyraclostrobin (F500 - Headline®; a.i. 20%) on the activity of nitrogenase in soybean (var. JS-335). Pyraclostrobin (F500) was applied on the leaves of soybean plants at 10 and 20 days after emergence (DAE) of seedlings at concentrations ranging from 0.05% to 1%. Leghemoglobin (Lb) content and nitrogenase activity in root nodules were analyzed at 45(th)day after emergence of seedlings indicated a remarkable increase in Lb content and enhanced activity of nitrogenase in the root nodules of pyraclostrobin treated plants. The fungicide also enhanced the number of nodules along with weight of nodules, root biomass and growth of shoot and leaves. Enhanced nitrogen fixation in the root nodules by pyraclostrobin improves the growth of the plant in soybean before flowering and pod formation which ultimately resulted in yield and yield attributes. These results suggest that pyraclostrobin (F500) can be successfully employed as a foliar spray under field conditions to enhance the growth, nitrogen assimilation and hence yield of soybean. Copyright © 2014 Elsevier Inc. All rights reserved.

Biological Control of Wheat Root Diseases by the CLP-Producing Strain Pseudomonas fluorescens HC1-07

PubMed Central

Yang, Ming-Ming; Wen, Shan-Shan; Mavrodi, Dmitri V.; Mavrodi, Olga V.; von Wettstein, Diter; Thomashow, Linda S.; Guo, Jian-Hua; Weller, David M.

2017-01-01

Pseudomonas fluorescens HC1-07, previously isolated from the phyllosphere of wheat grown in Hebei province, China, suppresses the soilborne disease of wheat take-all, caused by Gaeumannomyces graminis var. tritici. We report here that strain HC1-07 also suppresses Rhizoctonia root rot of wheat caused by Rhizoctonia solani AG-8. Strain HC1-07 produced a cyclic lipopeptide (CLP) with a molecular weight of 1,126.42 based on analysis by electrospray ionization mass spectrometry. Extracted CLP inhibited the growth of G. graminis var. tritici and R. solani in vitro. To determine the role of this CLP in biological control, plasposon mutagenesis was used to generate two nonproducing mutants, HC1-07viscB and HC1-07prtR2. Analysis of regions flanking plasposon insertions in HC1-07prtR2 and HC1-07viscB revealed that the inactivated genes were similar to prtR and viscB, respectively, of the well-described biocontrol strain P. fluorescens SBW25 that produces the CLP viscosin. Both genes in HC1-07 were required for the production of the viscosin-like CLP. The two mutants were less inhibitory to G. graminis var. tritici and R. solani in vitro and reduced in ability to suppress take-all. HC1-07viscB but not HC-07prtR2 was reduced in ability to suppress Rhizoctonia root rot. In addition to CLP production, prtR also played a role in protease production. PMID:24512115

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...

Influence of Pericarp, Cotyledon and Inhibitory Substances on Sharp Tooth Oak (Quercus aliena var. acuteserrata) Germination

PubMed Central

Liu, Yan; Liu, Guangquan; Li, Qingmei; Liu, Yong; Hou, Longyu; Li, GuoLei

2012-01-01

In order to explore the mechanism of delayed and uneven germination in sharp tooth oak (Quercus aliena var. acuteserrata) (STO), mechanical scarification techniques were used to study STO root and shoot germination and growth. The techniques used were: removing cup scar (RS), removing the pericarp (RP), and cutting off 1/2 (HC) and 2/3 (TC) cotyledons. Germination percentage and root and shoot length for Chinese cabbage (Beassica pekinensis) seeds (CCS) were also investigated for CCS cultivated in a Sanyo growth cabinet watered by distilled water and 80% methanol extracts from the acorn embryo, cotyledon and pericarp with concentrations of 1.0 g, 0.8 g, 0.6 g and 0.4 g dry acorn weight per ml methanol. The results showed that the majority of roots and shoots from acorns with RP and HC treatment emerged two weeks earlier, more simultaneously, and their total emergences were more than 46% and 28% higher, respectively. TC accelerated root and shoot emergence time and root length, but root and shoot germination rate and shoot height had no significant difference from the control. Positive consequences were not observed on all indices of RS treatment. The germination rates of CCS watered by 1.0 g·ml−1 methanol extracts from the embryo and cotyledon were significantly lower than those from the pericarp, and all concentrations resulted in decreased growth of root and shoot. Methanol extracts from pericarp significantly reduced root length of CCS, but presented little response in germination percentage and shoot length. The inhibitory effect was gradually increased with the increasing concentration of the methanol extract. We conclude that both the mechanical restriction of the pericarp and the presence of germination inhibitors in the embryo, cotyledon and pericarp are the causes for delayed and asynchronous germination of STO acorns. PMID:23133517

Drought effects on root and needle terpenoid content of a coastal and an interior Douglas fir provenance.

PubMed

Kleiber, Anita; Duan, Qiuxiao; Jansen, Kirstin; Verena Junker, Laura; Kammerer, Bernd; Rennenberg, Heinz; Ensminger, Ingo; Gessler, Arthur; Kreuzwieser, Jürgen

2017-12-01

Douglas fir (Pseudotsuga menziesii) is a conifer species that stores large amounts of terpenoids, mainly monoterpenoids in resin ducts of various tissues. The effects of drought on stored leaf terpenoid concentrations in trees are scarcely studied and published data are partially controversial, since reduced, unaffected or elevated terpenoid contents due to drought have been reported. Even less is known on the effect of drought on root terpenoids. In the present work, we investigated the effect of reduced water availability on the terpenoid content in roots and needles of Douglas fir seedlings. Two contrasting Douglas fir provenances were studied: an interior provenance (var. glauca) with assumed higher drought resistance, and a coastal provenance (var. menziesii) with assumed lower drought resistance. We tested the hypothesis that both provenances show specific patterns of stored terpenoids and that the patterns will change in response to drought in both, needles and roots. We further expected stronger changes in the less drought tolerant coastal provenance. For this purpose, we performed an experiment under controlled conditions, in which the trees were exposed to moderate and severe drought stress. According to our expectations, the study revealed clear provenance-specific terpenoid patterns in needles. However, such patterns were not detected in the roots. Drought slightly increased the needle terpenoid contents of the coastal but not of the interior provenance. We also observed increased terpenoid abundance mainly in roots of the moderately stressed coastal provenance. Overall, from the observed provenance-specific reactions with increased terpenoid levels in trees of the coastal origin in response to drought, we conclude on functions of terpenoids for abiotic stress tolerance that might be fulfilled by other, constitutively expressed mechanisms in drought-adapted interior provenances. © The Author 2017. Published by Oxford University Press. All rights

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.

Characterization of an antibiotic produced by a strain of Pseudomonas fluorescens inhibitory to Gaeumannomyces graminis var. tritici and Pythium spp.

PubMed Central

Gurusiddaiah, S; Weller, D M; Sarkar, A; Cook, R J

1986-01-01

The production, isolation, and characterization of an antibiotic substance from cultures of Pseudomonas fluorescens 2-79 (NRRL B-15132) is described. P. fluorescens 2-79 originally was isolated from the roots of wheat and is suppressive to the wheat root disease take-all caused by Gaeumannomyces graminis var. tritici. The antibiotic was isolated from potato glucose broth cultures of strain 2-79 by solvent extraction. It was purified by silica gel column chromatography and was a greenish yellow, needle-shaped crystal with a melting point of 242 degrees C (decomposition). It was soluble in methylene chloride, chloroform, acetone, 2 N sodium hydroxide, and 2 N hydrochloric acid and was insoluble in water, methanol, ethyl acetate, tetrahydrofuran, diethyl ether, carbon tetrachloride, hexane, and petroleum ether. On the basis of UV, infrared, 1H-nuclear magnetic resonance, 13C-nuclear magnetic resonance, mass spectral analysis, and elemental analysis, the structure of the antibiotic is proposed to be a dimer of phenazine carboxylic acid. Lithium aluminum hydride reduction of the antibiotic yielded hydroxymethyl phenazine as a major product which retained most of the biological characteristics of the parent molecule. There were no toxic symptoms when mice received this antibiotic by oral doses up to 464 mg/kg. The antibiotic showed excellent activity against several species of fungi, including the wheat pathogens Gaeumannomyces graminis var. tritici, Rhizoctonia solani, and Pythium aristosporum; and it may have a role in suppression of take-all in vivo by strain 2-79. PMID:3087284

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.

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

Distribution of calmodulin in corn seedlings - Immunocytochemical localization in coleoptiles and root apices

NASA Technical Reports Server (NTRS)

Dauwalder, M.; Roux, S. J.

1986-01-01

Immunofluorescence techniques have been used to study the distribution of calmodulin in several tissues in etiolated corn (Zea mays, var. Bear Hybrid) seedlings. Uniform staining was seen in the background cytoplasm of most cell types. Cell walls and vacuoles were not stained. In coleoptile mesophyll cells the nucleoplasm of most nuclei was stained as was the stroma of most amyloplasts. The lumen border of mature tracheary elements in coleoptiles also stained. In the rootcap the most intensely stained regions were the cytoplasms of columella cells and of the outermost cells enmeshed in the layer of secreted slime. Nuclei in the rootcap cells did not stain distinctly, but those in all cell types of the root meristem did. Also in the root meristem, the cytoplasm of metaxylem elements stained brightly. These results are compared and contrasted with previous data on the localization of calmodulin in pea root apices and epicotyls and discussed in relation to current hypotheses on mechanisms of gravitropism.

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.

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%.

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

Quantification of Coffea arabica and Coffea canephora var. robusta concentration in blends by means of synchronous fluorescence and UV-Vis spectroscopies.

PubMed

Dankowska, A; Domagała, A; Kowalewski, W

2017-09-01

The potential of fluorescence, UV-Vis spectroscopies as well as the low- and mid-level data fusion of both spectroscopies for the quantification of concentrations of roasted Coffea arabica and Coffea canephora var. robusta in coffee blends was investigated. Principal component analysis was used to reduce data multidimensionality. To calculate the level of undeclared addition, multiple linear regression (PCA-MLR) models were used with lowest root mean square error of calibration (RMSEC) of 3.6% and root mean square error of cross-validation (RMSECV) of 7.9%. LDA analysis was applied to fluorescence intensities and UV spectra of Coffea arabica, canephora samples, and their mixtures in order to examine classification ability. The best performance of PCA-LDA analysis was observed for data fusion of UV and fluorescence intensity measurements at wavelength interval of 60nm. LDA showed that data fusion can achieve over 96% of correct classifications (sensitivity) in the test set and 100% of correct classifications in the training set, with low-level data fusion. The corresponding results for individual spectroscopies ranged from 90% (UV-Vis spectroscopy) to 77% (synchronous fluorescence) in the test set, and from 93% to 97% in the training set. The results demonstrate that fluorescence, UV, and visible spectroscopies complement each other, giving a complementary effect for the quantification of roasted Coffea arabica and Coffea canephora var. robusta concentration in blends. Copyright © 2017 Elsevier B.V. All rights reserved.

Micropropagation of Araucaria excelsa R. Br. var. glauca Carrière from orthotropic stem explants.

PubMed

Sarmast, Mostafa Khoshhal; Salehi, Hassan; Khosh-Khui, Morteza

2012-07-01

The objectives of the present work were in vitro propagation of Araucaria excelsa R. Br. var. glauca Carrière (Norfolk Island pine) with focus on the evaluation of the mean number of shoots per explant (MNS/E) and mean length of shoots per explants (MLS/E) produced by different parts of the orthotropic stem of A. excelsa R. Br. var. glauca in response to plant growth regulators. Norfolk Island pine axillary meristems responded very well to the 2-iso-pentenyl adenine (2iP) and thidiazuron (TDZ) levels. Explants taken from stem upper segments in the media containing 2iP had a higher MNS/E (3.47) and MLS/E (6.27 mm) in comparison to those taken from stem lower segments, which were 0.71 and 0.51 mm, respectively. Using 0.045 μM TDZ in the MS medium not only resulted in 4.60 MNS/E with 7.08 mm MLS/E but proliferated shoots showed a good performance as well. Investigating the best position of stem explant on mother plant as well as the best concentrations of growth regulators were performed which were useful for efficient micropropagation of this plant. Thirty three percent of explants were rooted in the MS medium containing 3 % sucrose, supplemented with 7.5 μM of both NAA and IBA for 2 weeks before transferring to a half strength MS medium without any growth regulator. Plantlets obtained were acclimatized and transferred to the greenhouse with less than 20 % mortality. This procedure considered the first successful report for regeneration and acclimatization of A. excelsa R. Br. var. glauca plantlet through main stem explants.

Resistant Citrullus lanatus var. citroides Rootstocks for Managing Root-knot Nematodes in Grafted Watermelon

USDA-ARS?s Scientific Manuscript database

Southern root-knot nematode (RKN), Meloidogyne incognita, is an important re-emerging pest of watermelon. Several factors have contributed to re-emergence of RKN including: 1) ban of methyl bromide for soil fumigation; 2) reduced land area for crop rotation; and 3) continuous cropping of cucurbits u...

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.

[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.

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

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.

Impact of copper toxicity on stone-head cabbage (Brassica oleracea var. capitata) in hydroponics.

PubMed

Ali, Sajid; Shahbaz, Muhammad; Shahzad, Ahmad Naeem; Khan, Hafiz Azhar Ali; Anees, Moazzam; Haider, Muhammad Saleem; Fatima, Ammara

2015-01-01

Arable soils are frequently subjected to contamination with copper as the consequence of imbalanced fertilization with manure and organic fertilizers and/or extensive use of copper-containing fungicides. In the present study, the exposure of stone-head cabbage (Brassica oleracea var. capitata) to elevated Cu(2+) levels resulted in leaf chlorosis and lesser biomass yield at ≥2 µ M. Root nitrate content was not statistically affected by Cu(2+) levels, although it was substantially decreased at ≥5 µ M Cu(2+) in the shoot. The decrease in nitrate contents can be related to lower nitrate uptake rates because of growth inhibition by Cu-toxicity. Shoot sulfate content increased strongly at ≥2 µ M Cu(2+) indicating an increase in demand for sulfur under Cu stress. Furthermore, at ≥2 µM concentration, concentration of water-soluble non-protein thiol increased markedly in the roots and to a smaller level in the shoot. When exposed to elevated concentrations of Cu(2+) the improved sulfate and water-soluble non-protein thiols need further studies for the evaluation of their direct relation with the synthesis of metal-chelating compounds (i.e., phytochelatins).

Two Lactarius species associated with a relict Fagus grandifolia var. mexicana population in a Mexican montane cloud forest.

PubMed

Montoya, L; Haug, I; Bandala, V M

2010-01-01

Ectomycorrhizal (EM) fleshy fungi are being monitored in a population of Fagus grandifolia var. mexicana persisting in a montane cloud forest refuge on a volcano in a subtropical region of central Veracruz (eastern Mexico). The population of Fagus studied represents one of the 10 recognized forest fragments still housing this tree genus in Mexico. This is the first attempt to document EM fungi associated with this tree species in Mexico. We present evidence of the ectomycorrhizal symbiosis for Lactarius badiopallescens and L. cinereus with this endemic tree. Species identification of Lactarius on Fagus grandifolia var. mexicana was based on the comparison of DNAsequences (ITS rDNA) of spatiotemporally co-occurring basidiomes and EM root tips. The host of the EM tips was identified by comparison of the large subunit of the ribulose-bisphosphate carboxylase gene (rbcL). The occurrence of Lactarius badiopallescens and L. cinereus populations in the area of study represent the southernmost record known to date of these two species in North America and are new for the Neotropical Lactarius mycota. Descriptions coupled with illustrations of macro- and micromorphological features of basidiomes as well as photographs of ectomycorrhizas are presented.

Comparison of uptake, translocation and accumulation of several neonicotinoids in komatsuna (Brassica rapa var. perviridis) from contaminated soils.

PubMed

Li, Yong; Long, Ling; Yan, Huangqian; Ge, Jing; Cheng, Jinjin; Ren, Liyun; Yu, Xiangyang

2018-06-01

The accumulation of pesticides in vegetables may have serious effects on human health and ecosystems via food chains; therefore, it is of great importance to investigate the uptake and accumulation behaviours of pesticides in vegetable tissues. In the present study, the uptake, translocation and accumulation of five neonicotinoids, thiamethoxam (THIM), clothianidin (CLO), thiacloprid (THID), acetamiprid (ACE) and dinotefuran (DIN), in komatsuna (Brassica rapa var. perviridis, a vegetable) were investigated. The concentrations of neonicotinoids in vegetable tissues ranged from 0.068 ± 0.002 to 29.6 ± 2.5 mg/kg. During the cultivation (except for the first day), the concentration of each neonicotinoid in shoots was the highest, followed by roots and the soil. The concentrating of neonicotinoids from the soil to roots followed the order of THIM > CLO > THID > DIN > ACE, while the order of the ability of translocation neonicotinoids from roots to shoots was the just opposite. The difference in uptake and translocation behaviours of the test neonicotinoids seems to be not correlated with the octanol/water partition coefficient (logK ow ), water solubility or dissociation constant (pK a ), but significantly correlated with molecular weight. In addition, a greater concentration of the THIM-metabolite clothianidin (M-CLO) was detected in vegetable shoots than in roots and the soil. Copyright © 2018 Elsevier Ltd. 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.

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.

Influence of different irrigation levels on the root water uptake and the physiology of root-chicory

NASA Astrophysics Data System (ADS)

Vandoorne, B.; Dekoninck, N.; Lutts, S.; Capelle, B.; Javaux, M.

2009-04-01

In the context of global warming and given recent heat waves observed in Western Europe, the relationship between the soil water status and the plant health has recently received more attention, especially for cash crops like chicory. In this study we particularly investigated the impact of soil water status on the chicory root water uptake and density and made a link with physiological and yield parameters. During five months, we imposed different irrigation levels to 10 plants of chicory (Cichorium intybus var. sativum) growing in greenhouses. Each seed, coming from an autogamous selection in this allogamous species, was sown in a column of 1.42m height and 0.4m diameter filled with yellow sand and irrigated from the bottom with Hoagland solution. On those 10 columns, we measured the distribution of soil moisture with TDR (8 columns) and ERT (2 columns) probes. Lateral windows also allowed us to follow the root growth. The column weights were also monitored in order to quantify the plant transpiration. During the experiment, several physiological indices were also followed like the gas exchange (CO2 and transpiration), the chlorophyll fluorescence, the stomatal conductance, the plastochron, and the Leaf Area Index (LAI). At the end of the experiment, the complete root length density and the water content profiles were measured. We had also a look to the osmotic potential, the pigments content and the isotopic discrimination of carbon in the leaves, which gives information about the level of stress. At a biochemical point of view, we measured the content in enzymes involves in inulin metabolism and sugars synthesis. We observed that the plants suffering from a slight water stress developed better. A simple1-D model was built which describes the root growth in function of the irrigation level and of the soil and atmospheric boundary conditions.

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

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.

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.

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

Immunolocalization of IAA and ABA in roots and needles of radiata pine (Pinus radiata) during drought and rewatering.

PubMed

De Diego, N; Rodríguez, J L; Dodd, I C; Pérez-Alfocea, F; Moncaleán, P; Lacuesta, M

2013-05-01

Anatomical, physiological and phytohormonal changes involved in drought tolerance were examined in different Pinus radiata D. Don breeds subjected to soil drying and rewatering. Breeds with the smallest stomatal chamber size had the lowest transpiration rate and the highest intrinsic water-use efficiency. Xylem cell size was positively correlated with leaf hydraulic conductance and needle indole-3-acetic acid (IAA) concentrations, whereas transpiration rate was negatively correlated with needle abscisic acid (ABA) levels. Since these two phytohormones seem important in regulating the P. radiata drought response, they were simultaneously immunolocalized in roots and needles of the most tolerant breed (P. radiata var. radiata × var. cedrosensis) during two sequential drought cycles and after rewatering. During drought, IAA was unequally distributed into the pointed area of the needle cross-section and mainly located in mesophyll and vascular tissue cells of needles, possibly inducing needle epinasty, whereas ABA was principally located in guard cells, presumably to elicit stomata closure. In the roots, at the end of the first drought cycle, while strong IAA accumulation was observed in the cortex, ABA levels decreased probably due to translocation to the leaves. Rewatering modified the distribution of both IAA and ABA in the needles, causing an accumulation principally in vascular tissue, with residual concentrations in mesophyll, likely favouring the acclimatization of the plants for further drought cycles. Contrarily, in the roots IAA and ABA were located in the exodermis, a natural barrier that regulates the phytohormone translocation to other plant tissues and hormone losses to the soil solution after rewatering. These results confirm that immunolocalization is an efficient tool to understand the translocation of IAA and ABA in plants subjected to different water stress situations, and clarify their role in regulating physiological responses such as stomata

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...

Effects of rooting and tree growth of selected woodland species on cap integrity in a mineral capped landfill site.

PubMed

Hutchings, T R; Moffat, A J; Kemp, R A

2001-06-01

The above and below ground growth of three tree species (Alnus glutinosa, Pinus nigra var. maritima and Acer pseudoplatanus) was studied on a containment landfill site at Waterford, Hertfordshire, UK. Tree root architecture was studied using soil inspection pits excavated next to 12 trees of each species and mapped in detail. Tree height was related to soil thickness over the compacted mineral cap. No roots entered the cap where soil thickness was 1.3 m, but a few roots, especially of alder, were observed within it when the soil cover was 1.0 m or less. Micromorphological analysis of undisturbed samples of the mineral cap suggested that roots exploited weaknesses in the cap rather than actively causing penetration into it. Alder roots were more tolerant of anaerobic conditions within the cap than the other species examined. The results confirm that mineral caps should be covered by 1.5 m of soil or soil-forming material if tree establishment is intended over a restored landfill site, unless protected by other parts of a composite capping system.

Evaluation of precipitation forecasts from 3D-Var and hybrid GSI-based system during Indian summer monsoon 2015

NASA Astrophysics Data System (ADS)

Singh, Sanjeev Kumar; Prasad, V. S.

2018-02-01

This paper presents a systematic investigation of medium-range rainfall forecasts from two versions of the National Centre for Medium Range Weather Forecasting (NCMRWF)-Global Forecast System based on three-dimensional variational (3D-Var) and hybrid analysis system namely, NGFS and HNGFS, respectively, during Indian summer monsoon (June-September) 2015. The NGFS uses gridpoint statistical interpolation (GSI) 3D-Var data assimilation system, whereas HNGFS uses hybrid 3D ensemble-variational scheme. The analysis includes the evaluation of rainfall fields and comparisons of rainfall using statistical score such as mean precipitation, bias, correlation coefficient, root mean square error and forecast improvement factor. In addition to these, categorical scores like Peirce skill score and bias score are also computed to describe particular aspects of forecasts performance. The comparison results of mean precipitation reveal that both the versions of model produced similar large-scale feature of Indian summer monsoon rainfall for day-1 through day-5 forecasts. The inclusion of fully flow-dependent background error covariance significantly improved the wet biases in HNGFS over the Indian Ocean. The forecast improvement factor and Peirce skill score in the HNGFS have also found better than NGFS for day-1 through day-5 forecasts.

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.

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

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

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.

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.

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.

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.

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.

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

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

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…

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

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 .

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

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

Comparative effects of plant growth regulators on leaf and stem explants of Labisia pumila var. alata

PubMed Central

Ling, Anna Pick Kiong; Tan, Kinn Poay; Hussein, Sobri

2013-01-01

Objective: Labisia pumila var. alata, commonly known as ‘Kacip Fatimah’ or ‘Selusuh Fatimah’ in Southeast Asia, is traditionally used by members of the Malay community because of its post-partum medicinal properties. Its various pharmaceutical applications cause an excessive harvesting and lead to serious shortage in natural habitat. Thus, this in vitro propagation study investigated the effects of different plant growth regulators (PGRs) on in vitro leaf and stem explants of L. pumila. Methods: The capabilities of callus, shoot, and root formation were evaluated by culturing both explants on Murashige and Skoog (MS) medium supplemented with various PGRs at the concentrations of 0, 1, 3, 5, and 7 mg/L. Results: Medium supplemented with 3 mg/L indole-3-butyric acid (IBA) showed the optimal callogenesis from both leaf and stem explants with (72.34±19.55)% and (70.40±14.14)% efficacy, respectively. IBA was also found to be the most efficient PGR for root induction. A total of (50.00±7.07)% and (77.78±16.47)% of root formation were obtained from the in vitro stem and leaf explants after being cultured for (26.5±5.0) and (30.0±8.5) d in the medium supplemented with 1 and 3 mg/L of IBA, respectively. Shoot formation was only observed in stem explant, with the maximum percentage of formation ((100.00±0.00)%) that was obtained in 1 mg/L zeatin after (11.0±2.8) d of culture. Conclusions: Callus, roots, and shoots can be induced from in vitro leaf and stem explants of L. pumila through the manipulation of types and concentrations of PGRs. PMID:23825148

Rhizofiltration using sunflower (Helianthus annuus L.) and bean (Phaseolus vulgaris L. var. vulgaris) to remediate uranium contaminated groundwater.

PubMed

Lee, Minhee; Yang, Minjune

2010-01-15

The uranium removal efficiencies of rhizofiltration in the remediation of groundwater were investigated in lab-scale experiments. Sunflower (Helianthus annuus L.) and bean (Phaseolus vulgaris L. var. vulgaris) were cultivated and an artificially uranium contaminated solution and three genuine groundwater samples were used in the experiments. More than 80% of the initial uranium in solution and genuine groundwater, respectively, was removed within 24h by using sunflower and the residual uranium concentration of the treated water was lower than 30 microg/L (USEPA drinking water limit). For bean, the uranium removal efficiency of the rhizofiltration was roughly 60-80%. The maximum uranium removal via rhizofiltration for the two plant cultivars occurred at pH 3-5 of solution and their uranium removal efficiencies exceeded 90%. The lab-scale continuous rhizofiltration clean-up system delivered over 99% uranium removal efficiency, and the results of SEM and EDS analyses indicated that most uranium accumulated in the roots of plants. The present results suggested that the uranium removal capacity of two plants evaluated in the clean-up system was about 25mg/kg of wet plant mass. Notably, the removal capacity of the root parts only was more than 500 mg/kg.

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.

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.

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

Prioritizing quantitative trait loci for root system architecture in tetraploid wheat

PubMed Central

Maccaferri, Marco; El-Feki, Walid; Nazemi, Ghasemali; Salvi, Silvio; Canè, Maria Angela; Colalongo, Maria Chiara; Stefanelli, Sandra; Tuberosa, Roberto

2016-01-01

Optimization of root system architecture (RSA) traits is an important objective for modern wheat breeding. Linkage and association mapping for RSA in two recombinant inbred line populations and one association mapping panel of 183 elite durum wheat (Triticum turgidum L. var. durum Desf.) accessions evaluated as seedlings grown on filter paper/polycarbonate screening plates revealed 20 clusters of quantitative trait loci (QTLs) for root length and number, as well as 30 QTLs for root growth angle (RGA). Divergent RGA phenotypes observed by seminal root screening were validated by root phenotyping of field-grown adult plants. QTLs were mapped on a high-density tetraploid consensus map based on transcript-associated Illumina 90K single nucleotide polymorphisms (SNPs) developed for bread and durum wheat, thus allowing for an accurate cross-referencing of RSA QTLs between durum and bread wheat. Among the main QTL clusters for root length and number highlighted in this study, 15 overlapped with QTLs for multiple RSA traits reported in bread wheat, while out of 30 QTLs for RGA, only six showed co-location with previously reported QTLs in wheat. Based on their relative additive effects/significance, allelic distribution in the association mapping panel, and co-location with QTLs for grain weight and grain yield, the RSA QTLs have been prioritized in terms of breeding value. Three major QTL clusters for root length and number (RSA_QTL_cluster_5#, RSA_QTL_cluster_6#, and RSA_QTL_cluster_12#) and nine RGA QTL clusters (QRGA.ubo-2A.1, QRGA.ubo-2A.3, QRGA.ubo-2B.2/2B.3, QRGA.ubo-4B.4, QRGA.ubo-6A.1, QRGA.ubo-6A.2, QRGA.ubo-7A.1, QRGA.ubo-7A.2, and QRGA.ubo-7B) appear particularly valuable for further characterization towards a possible implementation of breeding applications in marker-assisted selection and/or cloning of the causal genes underlying the QTLs. PMID:26880749

Prioritizing quantitative trait loci for root system architecture in tetraploid wheat.

PubMed

Maccaferri, Marco; El-Feki, Walid; Nazemi, Ghasemali; Salvi, Silvio; Canè, Maria Angela; Colalongo, Maria Chiara; Stefanelli, Sandra; Tuberosa, Roberto

2016-02-01

Optimization of root system architecture (RSA) traits is an important objective for modern wheat breeding. Linkage and association mapping for RSA in two recombinant inbred line populations and one association mapping panel of 183 elite durum wheat (Triticum turgidum L. var. durum Desf.) accessions evaluated as seedlings grown on filter paper/polycarbonate screening plates revealed 20 clusters of quantitative trait loci (QTLs) for root length and number, as well as 30 QTLs for root growth angle (RGA). Divergent RGA phenotypes observed by seminal root screening were validated by root phenotyping of field-grown adult plants. QTLs were mapped on a high-density tetraploid consensus map based on transcript-associated Illumina 90K single nucleotide polymorphisms (SNPs) developed for bread and durum wheat, thus allowing for an accurate cross-referencing of RSA QTLs between durum and bread wheat. Among the main QTL clusters for root length and number highlighted in this study, 15 overlapped with QTLs for multiple RSA traits reported in bread wheat, while out of 30 QTLs for RGA, only six showed co-location with previously reported QTLs in wheat. Based on their relative additive effects/significance, allelic distribution in the association mapping panel, and co-location with QTLs for grain weight and grain yield, the RSA QTLs have been prioritized in terms of breeding value. Three major QTL clusters for root length and number (RSA_QTL_cluster_5#, RSA_QTL_cluster_6#, and RSA_QTL_cluster_12#) and nine RGA QTL clusters (QRGA.ubo-2A.1, QRGA.ubo-2A.3, QRGA.ubo-2B.2/2B.3, QRGA.ubo-4B.4, QRGA.ubo-6A.1, QRGA.ubo-6A.2, QRGA.ubo-7A.1, QRGA.ubo-7A.2, and QRGA.ubo-7B) appear particularly valuable for further characterization towards a possible implementation of breeding applications in marker-assisted selection and/or cloning of the causal genes underlying the QTLs. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Linking carbon supply to root cell-wall chemistry and mechanics at high altitudes in Abies georgei

PubMed Central

Genet, Marie; Li, Mingcai; Luo, Tianxiang; Fourcaud, Thierry; Clément-Vidal, Anne; Stokes, Alexia

2011-01-01

Background and Aims The mobile carbon supply to different compartments of a tree is affected by climate, but its impact on cell-wall chemistry and mechanics remains unknown. To understand better the variability in root growth and biomechanics in mountain forests subjected to substrate mass movement, we investigated root chemical and mechanical properties of mature Abies georgei var. smithii (Smith fir) growing at different elevations on the Tibet–Qinghai Plateau. Methods Thin and fine roots (0·1–4·0 mm in diameter) were sampled at three different elevations (3480, 3900 and 4330 m, the last corresponding to the treeline). Tensile resistance of roots of different diameter classes was measured along with holocellulose and non-structural carbon (NSC) content. Key Results The mean force necessary to break roots in tension decreased significantly with increasing altitude and was attributed to a decrease in holocellulose content. Holocellulose was significantly lower in roots at the treeline (29·5 ± 1·3 %) compared with those at 3480 m (39·1 ± 1·0 %). Roots also differed significantly in NSC, with 35·6 ± 4·1 mg g−1 dry mass of mean total soluble sugars in roots at 3480 m and 18·8 ± 2·1 mg g−1 dry mass in roots at the treeline. Conclusions Root mechanical resistance, holocellulose and NSC content all decreased with increasing altitude. Holocellulose is made up principally of cellulose, the biosynthesis of which depends largely on NSC supply. Plants synthesize cellulose when conditions are optimal and NSC is not limiting. Thus, cellulose synthesis in the thin and fine roots measured in our study is probably not a priority in mature trees growing at very high altitudes, where climatic factors will be limiting for growth. Root NSC stocks at the treeline may be depleted through over-demand for carbon supply due to increased fine root production or winter root growth. PMID:21186240

Effects of plant growth promoting bacteria and mycorrhizal on Capsicum annuum L. var. aviculare ([Dierbach] D'Arcy and Eshbaugh) germination under stressing abiotic conditions.

PubMed

Rueda-Puente, Edgar Omar; Murillo-Amador, Bernardo; Castellanos-Cervantes, T; García-Hernández, José Luís; Tarazòn-Herrera, Mario Antonio; Moreno Medina, Salomòn; Gerlach Barrera, Luis Ernesto

2010-08-01

Capsicum annuum var. aviculare to Tarahumara and Papago Indians and farmers of Sonora desert is a promising biological and commercial value as a natural resource from arid and semiarid coastal zones. Traditionally, apply synthetic fertilizers to compensate for soil nitrogen deficiency. However, indiscriminate use of these fertilizers might increase salinity. The inoculation by plant growth promoting bacteria (PGPB) and arbuscular mycorrhizal fungi (AMF) represents an alternative as potential bio fertilizer resources for salty areas. Seeds ecotypes from four areas of Sonora desert (Mazocahui, Baviacora, Arizpe, La Tortuga), in order to inoculate them with one species of PGPB and AMF. Two germination tests were carried out to study the effect of salinity, temperature regime (night/day) and inoculation with PGPB and AMF growth factors measured on germination (percentage and rate), plant height, root length, and produced biomass (fresh and dry matter). The results indicated that from four studied ecotypes, Mazocahui was the most outstanding of all, showing the highest germination under saline and non-saline conditions. However, the PGPB and AMF influenced the others variables evaluated. This study is the first step to obtain an ideal ecotype of C. a. var. aviculare, which grows in the northwest of México and promoting this type of microorganisms as an efficient and reliable biological product. Studies of the association of PGPB and AMF with the C. a. var. aviculare-Mazocahui ecotype are recommended to determine the extent to which these observations can be reproduced under field conditions. Copyright 2010 Elsevier Masson SAS. All rights reserved.

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

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...

Antilithiasic and Hypolipidaemic Effects of Raphanus sativus L. var. niger on Mice Fed with a Lithogenic Diet

PubMed Central

Castro-Torres, Ibrahim Guillermo; Naranjo-Rodríguez, Elia Brosla; Domínguez-Ortíz, Miguel Ángel; Gallegos-Estudillo, Janeth; Saavedra-Vélez, Margarita Virginia

2012-01-01

In Mexico, Raphanus sativus L. var. niger (black radish) has uses for the treatment of gallstones and for decreasing lipids serum levels. We evaluate the effect of juice squeezed from black radish root in cholesterol gallstones and serum lipids of mice. The toxicity of juice was analyzed according to the OECD guidelines. We used female C57BL/6 mice fed with a lithogenic diet. We performed histopathological studies of gallbladder and liver, and measured concentrations of cholesterol, HDL cholesterol and triglycerides. The juice can be considered bioactive and non-toxic; the lithogenic diet significantly induced cholesterol gallstones; increased cholesterol and triglycerides levels, and decreased HDL levels; gallbladder wall thickness increased markedly, showing epithelial hyperplasia and increased liver weight. After treatment with juice for 6 days, cholesterol gallstones were eradicated significantly in the gallbladder of mice; cholesterol and triglycerides levels decreased too, and there was also an increase in levels of HDL (P < 0.05). Gallbladder tissue continued to show epithelial hyperplasia and granulocyte infiltration; liver tissue showed vacuolar degeneration. The juice of black radish root has properties for treatment of cholesterol gallstones and for decreasing serum lipids levels; therefore, we confirm in a preclinical study the utility that people give it in traditional medicine. PMID:23093836

Differential responses of two broccoli (Brassica oleracea L. var Italica) cultivars to salinity and nutritional quality improvement.

PubMed

Zaghdoud, Chokri; Alcaraz-López, Carlos; Mota-Cadenas, César; Martínez-Ballesta, María del Carmen; Moreno, Diego A; Ferchichi, Ali; Carvajal, Micaela

2012-01-01

The comparative responses of two broccoli cultivars (Brassica oleracea var. Italica, cv. Parthenon and cv. Naxos) to a 15 d exposure to different NaCl levels were investigated. Salinity led to increased concentrations of Na(+) and Cl(-) ions in both cultivars, a disruption of the endogenous minerals levels in the shoots and roots-that varied with the cultivar and salt concentration-and decreases in the osmotic potential (Ψ(π)), root hydraulic conductance (L(0)), and stomatal conductance (G(s)). The reduced biomass of Naxos at moderate NaCl indicates greater sensitivity to salinity, compared with Parthenon. Parthenon accumulated more soluble sugars, for osmotic adjustment, whereas Naxos accumulated proline, which gave the two cultivars differing nutritional characteristics. The total glucosinolates (GSLs) content was not affected by salinity in Parthenon while it decreased significantly in Naxos as a consequence of the decrease in the indole GSL. However, Naxos accumulated more aliphatic GSLs under salt stress than Parthenon, which confers on this cultivar a greater nutritional value when cultivated under salinity.These results suggest that, at distinct salinity levels, each broccoli cultivar adopts a specific strategy, indicating the crucial role of the genetic background on the organoleptic and nutritional properties that each cultivar acquires.

Arsenic speciation in tissues of the hyperaccumulator P. calomelanos var. austroamericana using X-ray absorption spectroscopy.

PubMed

Kachenko, Anthony G; Gräfe, Markus; Singh, Balwant; Heald, Steve M

2010-06-15

The fate and chemical speciation of arsenic (As) during uptake, translocation, and storage by the As hyperaccumulating fern Pityrogramma calomelanos var. austroamericana (Pteridaceae) were examined using inductively coupled plasma-atomic emission spectrometry (ICP-AES) and synchrotron-based micro-X-ray absorption near edge structure (micro-XANES) and micro-X-ray fluorescence (micro-XRF) spectroscopies. Chemical analysis revealed total As concentration was ca. 6.5 times greater in young fronds (5845 mg kg(-1) dry weight (DW)) than in old fronds (903 mg kg(-1) DW). In pinnae, As concentration decreased from the base (6822 mg kg(-1) DW) to the apex (4301 mg kg(-1) DW) of the fronds. The results from micro-XANES and micro-XRF of living tissues suggested that more than 60% of arsenate (As(V)) absorbed was reduced to arsenite (As(III)) in roots, prior to transport through vascular tissues as As(V) and As(III). In pinnules, As(III) was the predominant redox species (72-90%), presumably as solvated, oxygen coordinated compounds. The presence of putative As(III)-sulphide (S(2-)) coordination throughout the fern tissues (4-25%) suggests that S(2-) functional groups may contribute in the biochemical reduction of As(V) to As(III) during uptake and transport at a whole-plant level. Organic arsenicals and thiol-rich compounds were not detected in the species and are unlikely to play a role in As hyperaccumulation in this fern. The study provides important insights into homeostatic regulation of As following As uptake in P. calomelanos var. austroamericana.

Inhibition of Phosphate Uptake in Corn Roots by Aluminum-Fluoride Complexes1

PubMed Central

Façanha, Arnoldo Rocha; Okorokova-Façanha, Anna L.

2002-01-01

F forms stable complexes with Al at conditions found in the soil. Fluoroaluminate complexes (AlFx) have been widely described as effective analogs of inorganic phosphate (Pi) in Pi-binding sites of several proteins. In this work, we explored the possibility that the phytotoxicity of AlFx reflects their activity as Pi analogs. For this purpose, 32P-labeled phosphate uptake by excised roots and plasma membrane H+-ATPase activity were investigated in an Al-tolerant variety of maize (Zea mays L. var. dwarf hybrid), either treated or not with AlFx. In vitro, AlFx competitively inhibited the rate of root phosphate uptake as well as the H+-ATPase activity. Conversely, pretreatment of seedlings with AlFx in vivo promoted no effect on the H+-ATPase activity, whereas a biphasic effect on Pi uptake by roots was observed. Although the initial rate of phosphate uptake by roots was inhibited by AlFx pretreatment, this situation changed over the following minutes as the rate of uptake increased and a pronounced stimulation in subsequent 32Pi uptake was observed. This kinetic behavior suggests a reversible and competitive inhibition of the phosphate transporter by fluoroaluminates. The stimulation of root 32Pi uptake induced by AlFx pretreatment was tentatively interpreted as a phosphate starvation response. This report places AlF3 and AlF4− among Al-phytotoxic species and suggests a mechanism of action where the accumulation of Pi-mimicking fluoroaluminates in the soil may affect the phosphate absorption by plants. The biochemical, physiological, and environmental significance of these findings is discussed. PMID:12177489

[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.

Effects of foliar selenite on the nutrient components of turnip (Brassica rapa var. rapa Linn.)

NASA Astrophysics Data System (ADS)

Li, Xiong; Li, Boqun; Yang, Yongping

2018-03-01

We administered foliar applications of 50, 100 and 200 mg L‑1 selenium (Se, selenite) on turnip (Brassica rapa var. rapa Linn.) and detected the changes in the main nutrient components in fleshy roots. Results showed that the foliar application of Se (Ⅳ) significantly increased the Se content in turnip, and Se (Ⅳ) positively affected the uptake of several mineral elements, including magnesium, phosphorus, iron, zinc, manganese and copper. Se (Ⅳ) treatments also improved the synthesis of protein and multiple amino acids instead of crude fat and total carbohydrate in turnip, indicating that the foliar application of Se (Ⅳ) could enhance Se biofortification in turnip and promote its nutritional value. We recommended 50–100 mg L‑1 Se treatment for foliar application on turnip based on the daily intake of Se for adults (96–139 µg person‑1 day‑1) and its favourable effects on the nutrient components of turnip.

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.

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.

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.

Soil compaction and organic matter affect conifer seedling nonmycorrhizal and ectomycorrhizal root tip abundance and diversity. Forest Service research paper

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

Amaranthus, M.P.; Page-Dumroese, D.; Harvey, A.

1996-05-01

Three levels of organic matter removal (bole only; bole and crowns; and bole, crowns, and forest floor) and three levels of mechanical soil compaction (no compaction, moderate compaction, and severe soil compaction) were studied as they influence Douglas-fir (Pseudotsuga menziesii var. glauca (Beissn.) Franco) and western white pine (Pinus monticola Dougl. ex D. Don) seedlings following outplanting. Moderate and severe soil compaction significantly reduced nonmycorrhizal root tip abundance on both Douglas-fir and western white pine seedlings (p less than or equal to 0.05). Ectomycorrhizal root tip abundance was significantly reduced on Douglas-fir seedlings in severely compacted areas with bole andmore » crowns and bole, crowns, and forest floor removed. Ectomycorrhizal diversity also was significantly reduced on Douglas-fir seedlings in all severely compacted areas.« less

[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.

[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.

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.

The chromoplasts of Or mutants of cauliflower (Brassica oleracea L. var. botrytis).

PubMed

Paolillo, D J; Garvin, D F; Parthasarathy, M V

2004-12-01

The Or mutation in cauliflower (Brassica oleracea L. var. botrytis) leads to abnormal accumulations of beta-carotene in orange chromoplasts, in tissues in which leucoplasts are characteristic of wild-type plants. Or chromoplasts were investigated by light microscopy of fresh materials and electron microscopy of glutaraldehyde- and potassium permanganate-fixed materials. Carotenoid inclusions in Or chromoplasts resemble those found in carrot root chromoplasts in their optical activity and angular shape. Electron microscopy revealed that the inclusions are made up of parallel, membrane-bound compartments. These stacks of membranes are variously rolled and folded into three-dimensional objects. We classify Or chromoplasts as "membranous" chromoplasts. The Or mutation also limits plastid replication so that a single chromoplast constitutes the plastidome in most of the affected cells. There are one to two chromoplasts in each cell of a shoot apex. The ability of differentiated chromoplasts to divide in the apical meristems of Or mutant plants resembles the ability of proplastids to maintain plastid continuity from cell to cell in meristems of Arabidopsis thaliana mutants in which plastid replication is drastically limited. The findings are used to discuss the number of levels of regulation involved in plastid replication.

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.

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.

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

The root economics spectrum: divergence of absorptive root strategies with root diameter

NASA Astrophysics Data System (ADS)

Kong, D.; Wang, J.; Kardol, P.; Wu, H.; Zeng, H.; Deng, X.; Deng, Y.

2015-08-01

Plant roots usually vary along a dominant ecological axis, the root economics spectrum (RES), depicting a tradeoff between resource acquisition and conservation. For absorptive roots, which are mainly responsible for resource acquisition, we hypothesized that root strategies as predicted from the RES shift with increasing root diameter. To test this hypothesis, we used seven contrasting plant species for which we separated absorptive roots into two categories: thin roots (< 247 μm diameter) and thick roots. For each category, we analyzed a~range of root traits closely related to resource acquisition and conservation, including root tissue density, carbon (C) and nitrogen (N) fractions as well as root anatomical traits. The results showed that trait relationships for thin absorptive roots followed the expectations from the RES while no clear trait relationships were found in support of the RES for thick absorptive roots. Our results suggest divergence of absorptive root strategies in relation to root diameter, which runs against a single economics spectrum for absorptive roots.

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

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.

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.

Relationships between root diameter, root length and root branching along lateral roots in adult, field-grown maize

PubMed Central

Wu, Qian; Pagès, Loïc; Wu, Jie

2016-01-01

Background and Aims Root diameter, especially apical diameter, plays an important role in root development and function. The variation in diameter between roots, and along roots, affects root structure and thus the root system’s overall foraging performance. However, the effect of diameter variation on root elongation, branching and topological connections has not been examined systematically in a population of high-order roots, nor along the roots, especially for mature plants grown in the field. Methods A method combining both excavation and analysis was applied to extract and quantify root architectural traits of adult, field-grown maize plants. The relationships between root diameter and other root architectural characteristics are analysed for two maize cultivars. Key Results The basal diameter of the lateral roots (orders 1–3) was highly variable. Basal diameter was partly determined by the diameter of the bearing segment. Basal diameter defined a potential root length, but the lengths of most roots fell far short of this. This was explained partly by differences in the pattern of diameter change along roots. Diameter tended to decrease along most roots, with the steepness of the gradient of decrease depending on basal diameter. The longest roots were those that maintained (or sometimes increased) their diameters during elongation. The branching density (cm–1) of laterals was also determined by the diameter of the bearing segment. However, the location of this bearing segment along the mother root was also involved – intermediate positions were associated with higher densities of laterals. Conclusions The method used here allows us to obtain very detailed records of the geometry and topology of a complex root system. Basal diameter and the pattern of diameter change along a root were associated with its final length. These relationships are especially useful in simulations of root elongation and branching in source–sink models. PMID:26744490

Mutant selection in the self-incompatible plant radish (Raphanus sativus L. var. sativus) using two-step TILLING

PubMed Central

Kohzuma, Kaori; Chiba, Motoko; Nagano, Soichiro; Anai, Toyoaki; Ueda, Miki U.; Oguchi, Riichi; Shirai, Kazumasa; Hanada, Kousuke; Hikosaka, Kouki; Fujii, Nobuharu

2017-01-01

Radish (Raphanus sativus L. var. sativus), a widely cultivated root vegetable crop, possesses a large sink organ (the root), implying that photosynthetic activity in radish can be enhanced by altering both the source and sink capacity of the plant. However, since radish is a self-incompatible plant, improved mutation-breeding strategies are needed for this crop. TILLING (Targeting Induced Local Lesions IN Genomes) is a powerful method used for reverse genetics. In this study, we developed a new TILLING strategy involving a two-step mutant selection process for mutagenized radish plants: the first selection is performed to identify a BC1M1 line, that is, progenies of M1 plants crossed with wild-type, and the second step is performed to identify BC1M1 individuals with mutations. We focused on Rubisco as a target, since Rubisco is the most abundant plant protein and a key photosynthetic enzyme. We found that the radish genome contains six RBCS genes and one pseudogene encoding small Rubisco subunits. We screened 955 EMS-induced BC1M1 lines using our newly developed TILLING strategy and obtained six mutant lines for the six RsRBCS genes, encoding proteins with four different types of amino acid substitutions. Finally, we selected a homozygous mutant and subjected it to physiological measurements. PMID:28744180

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.

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.

Automated Root Tracking with "Root System Analyzer"

NASA Astrophysics Data System (ADS)

Schnepf, Andrea; Jin, Meina; Ockert, Charlotte; Bol, Roland; Leitner, Daniel

2015-04-01

Crucial factors for plant development are water and nutrient availability in soils. Thus, root architecture is a main aspect of plant productivity and needs to be accurately considered when describing root processes. Images of root architecture contain a huge amount of information, and image analysis helps to recover parameters describing certain root architectural and morphological traits. The majority of imaging systems for root systems are designed for two-dimensional images, such as RootReader2, GiA Roots, SmartRoot, EZ-Rhizo, and Growscreen, but most of them are semi-automated and involve mouse-clicks in each root by the user. "Root System Analyzer" is a new, fully automated approach for recovering root architectural parameters from two-dimensional images of root systems. Individual roots can still be corrected manually in a user interface if required. The algorithm starts with a sequence of segmented two-dimensional images showing the dynamic development of a root system. For each image, morphological operators are used for skeletonization. Based on this, a graph representation of the root system is created. A dynamic root architecture model helps to determine which edges of the graph belong to an individual root. The algorithm elongates each root at the root tip and simulates growth confined within the already existing graph representation. The increment of root elongation is calculated assuming constant growth. For each root, the algorithm finds all possible paths and elongates the root in the direction of the optimal path. In this way, each edge of the graph is assigned to one or more coherent roots. Image sequences of root systems are handled in such a way that the previous image is used as a starting point for the current image. The algorithm is implemented in a set of Matlab m-files. Output of Root System Analyzer is a data structure that includes for each root an identification number, the branching order, the time of emergence, the parent

[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.

Maize Root Phytase (Purification, Characterization, and Localization of Enzyme Activity and Its Putative Substrate).

PubMed Central

Hubel, F.; Beck, E.

1996-01-01

Three phytase (EC 3.1.3.26) isoforms from the roots of 8-d-old maize (Zea mays L. var Consul) seedlings were separated from phosphatases and purified to near homogeneity. The molecular mass of the native protein was 71 kD, and the isoelectric points of the three isoforms were pH 5.0, 4.9, and 4.8. Each of the three isoforms consisted of two subunits with a molecular mass of 38 kD. The temperature and pH optima (40[deg]C, pH 5.0) of these three isoforms, as well as the apparent Michaelis constants for sodium inositol hexakisphosphate (phytate) (43, 25, and 24 [mu]M) as determined by the release of inorganic phosphate, were only slightly different. Phytate concentrations higher than 300 [mu]M were inhibitory to all three isoforms. In contrast, the dephosphorylation of 4-nitrophenyl phosphate was not inhibited by any substrate concentration, but the Michaelis constants for this substrate were considerably higher (137-157 [mu]M). Hydrolysis of phytate by the phytase isoforms is a nonrandom reaction. D/L-Inositol-1,2,3,4,5- pentakisphosphate was identified as the first and D/L-inositol-1,2,5,6-tetrakisphosphate as the second intermediate in phytate hydrolysis. Phytase activity was localized in root slices. Although phosphatase activity was present in the stele and the cortex of the primary root, phytase activity was confined to the endodermis. Phytate was identified as the putative native substrate in maize roots (45 [mu]g P g-1 dry matter). It was readily labeled upon supplying [32P]phosphate to the roots. PMID:12226456

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.

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...

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

Morphological and molecular identification of the ectomycorrhizal association of Lactarius fumosibrunneus and Fagus grandifolia var. mexicana trees in eastern Mexico.

PubMed

Garay-Serrano, Edith; Bandala, Victor Manuel; Montoya, Leticia

2012-11-01

A population of Fagus grandifolia var. mexicana (covering ca. 4.7 ha) is established in a montane cloud forest refuge at Acatlan Volcano in eastern Mexico (Veracruz State), and it represents one of only ten populations of this species known to occur in the country (each stand covers ca. 2-35 ha in extension) and one of the southernmost in the continent. Sporocarps of several ectomycorrhizal macrofungi have been observed in the area, and among them, individuals of the genus Lactarius are common in the forest. However, the morphological and molecular characterization of ectomycorrhizae is still in development. Currently, two species of Lactarius have been previously documented in the area. Through the phylogenetic analysis of the internal transcribed spacer (ITS) region from basidiomes and ectomycorrhizae, we identified the Lactarius fumosibrunneus ectomycorrhiza. The host, F. grandifolia var. mexicana, was determined comparing the amplified ITS sequence from ectomycorrhizal root tips in the GenBank database with Basic Local Alignment Search Tool. The mycorrhizal system of L. fumosibrunneus is monopodial-pyramidal, characterized by its shiny, white to silver and pruinose surface, secreting a white latex when damaged, composed of three plectenchymatous mantle layers, with diverticulated terminal elements at the outer mantle. It lacks emanating hyphae, rhizomorphs, and sclerotia. A detailed morphological and anatomical description, illustrations, and photographs of the ectomycorrhiza are presented. The comparison of L. fumosibrunneus and other Lactarius belonging to subgenus Plinthogalus is presented.

GmPGIP3 enhanced resistance to both take-all and common root rot diseases in transgenic wheat.

PubMed

Wang, Aiyun; Wei, Xuening; Rong, Wei; Dang, Liang; Du, Li-Pu; Qi, Lin; Xu, Hui-Jun; Shao, Yanjun; Zhang, Zengyan

2015-05-01

Take-all (caused by the fungal pathogen Gaeumannomyces graminis var. tritici, Ggt) and common root rot (caused by Bipolaris sorokiniana) are devastating root diseases of wheat (Triticum aestivum L.). Development of resistant wheat cultivars has been a challenge since no resistant wheat accession is available. GmPGIP3, one member of polygalacturonase-inhibiting protein (PGIP) family in soybean (Glycine max), exhibited inhibition activity against fungal endopolygalacturonases (PGs) in vitro. In this study, the GmPGIP3 transgenic wheat plants were generated and used to assess the effectiveness of GmPGIP3 in protecting wheat from the infection of Ggt and B. sorokiniana. Four independent transgenic lines were identified by genomic PCR, Southern blot, and reverse transcription PCR (RT-PCR). The introduced GmPGIP3 was integrated into the genomes of these transgenic lines and could be expressed. The expressing GmPGIP3 protein in these transgenic wheat lines could inhibit the PGs produced by Ggt and B. sorokiniana. The disease response assessments postinoculation showed that the GmPGIP3-expressing transgenic wheat lines displayed significantly enhanced resistance to both take-all and common root rot diseases caused by the infection of Ggt and B. sorokiniana. These data suggested that GmPGIP3 is an attractive gene resource in improving resistance to both take-all and common root rot diseases in wheat.

Phytoextraction potential of poplar (Populus alba L. var. pyramidalis Bunge) from calcareous agricultural soils contaminated by cadmium.

PubMed

Hu, Yahu; Nan, Zhongren; Jin, Cheng; Wang, Ning; Luo, Huanzhang

2014-01-01

To investigate the phytoextraction potential of Populus alba L. var. pyramidalis Bunge for cadmium (Cd) contaminated calcareous soils, a concentration gradient experiment and a field sampling experiment (involving poplars of different ages) were conducted. The translocation factors for all experiments and treatments were greater than 1. The bioconcentration factor decreased from 2.37 to 0.25 with increasing soil Cd concentration in the concentration gradient experiment and generally decreased with stand age under field conditions. The Cd concentrations in P. pyramidalis organs decreased in the order of leaves > stems > roots. The shoot biomass production in the concentration gradient experiment was not significantly reduced with soil Cd concentrations up to or slightly over 50 mg kg(-1). The results show that the phytoextraction efficiency of P. pyramidalis depends on both the soil Cd concentration and the tree age. Populus pyramidalis is most suitable for remediation of slightly Cd contaminated calcareous soils through the combined harvest of stems and leaves under actual field conditions.

[Leishmaniasis transmission focus in El Hobo, Carmen de Bolívar, Bolívar, Colombia].

PubMed

Cortés, Luis Alberto

2006-10-01

The epidemiological characteristics and the importance of the Lutzomyia species present in a leishmaniasis focus in the village El Hobo, Carmen de Bolívar, Department of Bolivar, Colombia, are described. To obtain a preliminary assessment of leishmaniasis transmission in the village of El Hobo, Carmen de Bolívar. Epidemiological data were analyzed and sandflies were collected with CDC traps and on protected human volunteers in the village of El Hobo. Sero prevalence of canine visceral leishmaniasis in dogs was evaluated using indirect inmunofluorescence (IFAT). Nine Lutzomyia species were collected: L. trinidadensis, L. evansi, L. cayennensis, L. venezuelensis, L. gomezi, L. dubitans, L. ylephiletor, L. yuilli, and L. walkeri. The species of greater importance based on their implication in the transmission of cutaneous and visceral leishmaniasis were L. gomezi, and L. evansi respectively. Specimens of L. venezuelensis, L. dubitans, L. ylephiletor, L. yuilli, and L. walkeri are reported for the first time for the Department of Bolivar. The sero prevalence of visceral leishmaniasis in dogs was 36%. According to the epidemiological records, in 2002 the municipality of Carmen de Bolivar presented a 40% increase in cases of cutaneous leishmaniasis and an 80% increase in canine visceral leishmaniasis as compared to 2001, due to the outbreak in the village of El Hobo. The results indicate that the village of El Hobo is an area of potential risk for transmission of both cutaneous and visceral leishmaniasis.

Reduced ABA Accumulation in the Root System is Caused by ABA Exudation in Upland Rice (Oryza sativa L. var. Gaoshan1) and this Enhanced Drought Adaptation.

PubMed

Shi, Lu; Guo, Miaomiao; Ye, Nenghui; Liu, Yinggao; Liu, Rui; Xia, Yiji; Cui, Suxia; Zhang, Jianhua

2015-05-01

Lowland rice (Nipponbare) and upland rice (Gaoshan 1) that are comparable under normal and moderate drought conditions showed dramatic differences in severe drought conditions, both naturally occurring long-term drought and simulated rapid water deficits. We focused on their root response and found that enhanced tolerance of upland rice to severe drought conditions was mainly due to the lower level of ABA in its roots than in those of the lowland rice. We first excluded the effect of ABA biosynthesis and catabolism on root-accumulated ABA levels in both types of rice by monitoring the expression of four OsNCED genes and two OsABA8ox genes. Next, we excluded the impact of the aerial parts on roots by suppressing leaf-biosynthesized ABA with fluridone and NDGA (nordihydroguaiaretic acid), and measuring the ABA level in detached roots. Instead, we proved that upland rice had the ability to export considerably more root-sourced ABA than lowland rice under severe drought, which improved ABA-dependent drought adaptation. The investigation of apoplastic pH in root cells and root anatomy showed that ABA leakage in the root system of upland rice was related to high apoplastic pH and the absence of Casparian bands in the sclerenchyma layer. Finally, taking some genes as examples, we predicted that different ABA levels in rice roots stimulated distinct ABA perception and signaling cascades, which influenced its response to water stress. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

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.

[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.

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

Phytoremediation potential of transplanted bare-root seedlings of trees for lead/zinc and copper mine tailings.

PubMed

Shi, Xiang; Chen, Yi-Tai; Wang, Shu-Feng; Pan, Hong-Wei; Sun, Hai-Jing; Liu, Cai-Xia; Liu, Jian-Feng; Jiang, Ze-Ping

2016-11-01

Selecting plant species that can overcome unfavorable conditions and increase the recovery of degraded mined lands remains a challenge. A pot experiment was conducted to evaluate the feasibility of using transplanted tree seedlings for the phytoremediation of lead/zinc and copper mine tailings. One-year-old bare-root of woody species (Rhus chinensis Mill, Quercus acutissima Carruth, Liquidambar formosana Hance, Vitex trifolia Linn. var. simplicifolia Cham, Lespedeza cuneata and Amorpha fruticosa Linn) were transplanted into pots with mine tailings and tested as potential metal-tolerant plants. Seedling survival, plant growth, root trait, nutrient uptake, and metal accumulation and translocation were assessed. The six species grew in both tailings and showed different tolerance level. A. fruticosa was highly tolerant of Zn, Pb and Cu, and grew normally in both tailings. Metal concentrations were higher in the roots than in the shoots of the six species. All of the species had low bioconcentration and translocation factor values. However, R. chinensis and L. formosana had significantly higher translocation factor values for Pb (0.88) and Zn (1.78) than the other species. The nitrogen-fixing species, A. fruticosa, had the highest tolerance and biomass production, implying that it has great potential in the phytoremediation of tailing areas in southern China.

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

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.

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

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.

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.

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.

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

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...

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

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.

[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.

[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.

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.

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

Root architecture simulation improves the inference from seedling root phenotyping towards mature root systems.

PubMed

Zhao, Jiangsan; Bodner, Gernot; Rewald, Boris; Leitner, Daniel; Nagel, Kerstin A; Nakhforoosh, Alireza

2017-02-01

Root phenotyping provides trait information for plant breeding. A shortcoming of high-throughput root phenotyping is the limitation to seedling plants and failure to make inferences on mature root systems. We suggest root system architecture (RSA) models to predict mature root traits and overcome the inference problem. Sixteen pea genotypes were phenotyped in (i) seedling (Petri dishes) and (ii) mature (sand-filled columns) root phenotyping platforms. The RSA model RootBox was parameterized with seedling traits to simulate the fully developed root systems. Measured and modelled root length, first-order lateral number, and root distribution were compared to determine key traits for model-based prediction. No direct relationship in root traits (tap, lateral length, interbranch distance) was evident between phenotyping systems. RootBox significantly improved the inference over phenotyping platforms. Seedling plant tap and lateral root elongation rates and interbranch distance were sufficient model parameters to predict genotype ranking in total root length with an RSpearman of 0.83. Parameterization including uneven lateral spacing via a scaling function substantially improved the prediction of architectures underlying the differently sized root systems. We conclude that RSA models can solve the inference problem of seedling root phenotyping. RSA models should be included in the phenotyping pipeline to provide reliable information on mature root systems to breeding research. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Root architecture simulation improves the inference from seedling root phenotyping towards mature root systems

PubMed Central

Zhao, Jiangsan; Rewald, Boris; Leitner, Daniel; Nagel, Kerstin A.; Nakhforoosh, Alireza

2017-01-01

Abstract Root phenotyping provides trait information for plant breeding. A shortcoming of high-throughput root phenotyping is the limitation to seedling plants and failure to make inferences on mature root systems. We suggest root system architecture (RSA) models to predict mature root traits and overcome the inference problem. Sixteen pea genotypes were phenotyped in (i) seedling (Petri dishes) and (ii) mature (sand-filled columns) root phenotyping platforms. The RSA model RootBox was parameterized with seedling traits to simulate the fully developed root systems. Measured and modelled root length, first-order lateral number, and root distribution were compared to determine key traits for model-based prediction. No direct relationship in root traits (tap, lateral length, interbranch distance) was evident between phenotyping systems. RootBox significantly improved the inference over phenotyping platforms. Seedling plant tap and lateral root elongation rates and interbranch distance were sufficient model parameters to predict genotype ranking in total root length with an RSpearman of 0.83. Parameterization including uneven lateral spacing via a scaling function substantially improved the prediction of architectures underlying the differently sized root systems. We conclude that RSA models can solve the inference problem of seedling root phenotyping. RSA models should be included in the phenotyping pipeline to provide reliable information on mature root systems to breeding research. PMID:28168270

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

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...

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.

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.

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.

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.

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

[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.

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

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.

Comparison of HeNe laser and sinusoidal non-uniform magnetic field seed pre-sowing treatment effect on Glycine max (Var 90-I) germination, growth and yield.

PubMed

Asghar, Tehseen; Iqbal, Munawar; Jamil, Yasir; Zia-Ul-Haq; Nisar, Jan; Shahid, Muhammad

2017-01-01

Recently, laser and magnetic field pre-sowing seed treatments attracted the attention of the scientific community in response to their positive effect on plant characteristics and the present study was exemplified for Glycine max Var 90-I. Seeds were exposed to laser (HeNe-wave length 632nm and density power of 1mW/cm 2 ) and magnetic field (sinusoidal non-uniform-50, 75 and 100mT for 3, 5min with exposure) and seed germination, seedling growth and yield attributes were compared. The germination (mean germination, germination percentage, emergence index, germination speed, relative germination coefficient, emergence coefficient of uniformity) growth (root dry weight, root length, shoot fresh weight and shoot dry weight, leaf dry & fresh weight, root fresh weight, leaf area, shoot length, plant total dry weight at different stages, stem diameter, number of leaves, vigor index I & II), biochemical (essential oil) and yield attributes (seed weight, count) were enhanced significantly in response to both laser and magnetic field treatments. However, magnetic field treatment furnished slightly higher response versus laser except relative water contents, whole plant weight and shoot length. Results revealed that both laser and magnetic field pre-sowing seed treatments affect the germination, seedling growth, and yield characteristics positively and could possibly be used to enhance Glycine max productivity. Copyright © 2016 Elsevier B.V. All rights reserved.

Root architecture impacts on root decomposition rates in switchgrass

NASA Astrophysics Data System (ADS)

de Graaff, M.; Schadt, C.; Garten, C. T.; Jastrow, J. D.; Phillips, J.; Wullschleger, S. D.

2010-12-01

Roots strongly contribute to soil organic carbon accrual, but the rate of soil carbon input via root litter decomposition is still uncertain. Root systems are built up of roots with a variety of different diameter size classes, ranging from very fine to very coarse roots. Since fine roots have low C:N ratios and coarse roots have high C:N ratios, root systems are heterogeneous in quality, spanning a range of different C:N ratios. Litter decomposition rates are generally well predicted by litter C:N ratios, thus decomposition of roots may be controlled by the relative abundance of fine versus coarse roots. With this study we asked how root architecture (i.e. the relative abundance of fine versus coarse roots) affects the decomposition of roots systems in the biofuels crop switchgrass (Panicum virgatum L.). To understand how root architecture affects root decomposition rates, we collected roots from eight switchgrass cultivars (Alamo, Kanlow, Carthage, Cave-in-Rock, Forestburg, Southlow, Sunburst, Blackwell), grown at FermiLab (IL), by taking 4.8-cm diameter soil cores from on top of the crown and directly next to the crown of individual plants. Roots were carefully excised from the cores by washing and analyzed for root diameter size class distribution using WinRhizo. Subsequently, root systems of each of the plants (4 replicates per cultivar) were separated in 'fine' (0-0.5 mm), 'medium' (0.5-1 mm) and 'coarse' roots (1-2.5 mm), dried, cut into 0.5 cm (medium and coarse roots) and 2 mm pieces (fine roots), and incubated for 90 days. For each of the cultivars we established five root-treatments: 20g of soil was amended with 0.2g of (1) fine roots, (2) medium roots, (3) coarse roots, (4) a 1:1:1 mixture of fine, medium and coarse roots, and (5) a mixture combining fine, medium and coarse roots in realistic proportions. We measured CO2 respiration at days 1, 3, 7, 15, 30, 60 and 90 during the experiment. The 13C signature of the soil was -26‰, and the 13C signature

Essential oils and crude extracts from Chrysanthemum trifurcatum leaves, stems and roots: chemical composition and antibacterial activity.

PubMed

Sassi, Ahlem Ben; Skhiri, Fethia Harzallah; Chraief, Imed; Bourgougnon, Nathalie; Hammami, Mohamed; Aouni, Mahjoub

2014-01-01

The essential oils from the leaves, stems and roots of Chrysanthemum trifurcatum (Desf.) Batt. and Trab. var. macrocephalum (viv.) were obtained by hydrodistillation and their chemical compositions were analysed by gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS), in order to get insight into similarities and differences as to their active composition. A total of fifty compounds were identified, constituting 97.84%, 99.02% and 98.20% of total oil composition of the leaves, stems and roots, respectively. Monoterpene hydrocarbons were shown to be the main group of constituents of the leaves and stems parts in the ratio of 67.88% and 51.29%, respectively. But, the major group in the roots oil was found to be sesquiterpene hydrocarbons (70.30%). The main compounds in leaves oil were limonene (26.83%), γ-terpinene (19.68%), α-pinene (9.7%) and α-terpenyl acetate (7.16%). The stems oil, contains mainly limonene (32.91%), 4-terpenyl acetate (16.33%) and γ-terpinene (5.93%), whereas the main compounds in roots oil were α-calacorene (25.98%), α-cedrene (16.55%), β-bourbobene (14.91%), elemol (7.45%) and 2-hexenal (6.88%). The crude organic extracts of leaves, stems and roots, obtained by maceration with solvents of increasing polarity: petroleum ether, ethyl acetate and methanol, contained tannins, flavonoids and alkaloids. Meanwhile, essential oils and organic extracts were tested for antibacterial activities against eight Gram-positive and Gram-negative strains, using a microdilution method. The oil and methanolic extact from C. trifurcatum leaves showed a great potential of antibacterial effect against Bacillus subtilis and Staphylococcus epidermidis, with an IC50 range of 31.25-62.5 µg/ml.

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.

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.

Root rots

Treesearch

Kathryn Robbins; Philip M. Wargo

1989-01-01

Root rots of central hardwoods are diseases caused by fungi that infect and decay woody roots and sometimes also invade the butt portion of the tree. By killing and decaying roots, root rotting fungi reduce growth, decrease tree vigor, and cause windthrow and death. The most common root diseases of central hardwoods are Armillaria root rot, lnonotus root rot, and...

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

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

Water-soluble polysaccharides from Pleurotus ostreatus var. florida mycelial biomass.

PubMed

Komura, Dirce L; Ruthes, Andrea C; Carbonero, Elaine R; Gorin, Philip A J; Iacomini, Marcello

2014-09-01

Pleurotus ostreatus var. florida known as Hiratake has a high nutritional value, presents medicinal and nutraceutical properties and it is one of the consumed mushrooms in Brazil. Thus, the aim of this study was to characterize the chemical structure of polysaccharides found in mycelial biomass produced by submerged culture of P. ostreatus var. florida in order to compare with those found in P. ostreatus var. florida fruit bodies. Aqueous and alkali extracts obtained from mycelial biomass were purified, 13C NMR, GC-MS and chemical techniques were used to characterize three polysaccharide structures: a mannogalactan (MG-PfM) with α-D-Galp and 3-O-Me-α-D-Galp units, both (1→6)-linked, highly substituted at O-2 by D-Manp, a glycogen-like polymer (GLY-PfM) with α-D-Glp (1→4)-linked main chain, partially substituted at O-6 by α-D-Glcp side chains and a (1→3), (1→6) β-D-glucan (βGLC-PfM) with a main chain of β-D-Glcp (1→3)-linked units, partially substituted at O-6 by side chains of 6-O-substituted β-D-glucopyranosyl units, on an average of one to every two residues of the backbone. These results show the possibility to obtain similar and also different molecules from those found in the fruiting body of the same mushroom species, therefore the submerged culture of mushroom is a promising way to give raise molecules of interest. Copyright © 2014. Published by Elsevier B.V.

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.

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

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

Root hairs improve root penetration, root-soil contact, and phosphorus acquisition in soils of different strength.

PubMed

Haling, Rebecca E; Brown, Lawrie K; Bengough, A Glyn; Young, Iain M; Hallett, Paul D; White, Philip J; George, Timothy S

2013-09-01

Root hairs are a key trait for improving the acquisition of phosphorus (P) by plants. However, it is not known whether root hairs provide significant advantage for plant growth under combined soil stresses, particularly under conditions that are known to restrict root hair initiation or elongation (e.g. compacted or high-strength soils). To investigate this, the root growth and P uptake of root hair genotypes of barley, Hordeum vulgare L. (i.e. genotypes with and without root hairs), were assessed under combinations of P deficiency and high soil strength. Genotypes with root hairs were found to have an advantage for root penetration into high-strength layers relative to root hairless genotypes. In P-deficient soils, despite a 20% reduction in root hair length under high-strength conditions, genotypes with root hairs were also found to have an advantage for P uptake. However, in fertilized soils, root hairs conferred an advantage for P uptake in low-strength soil but not in high-strength soil. Improved root-soil contact, coupled with an increased supply of P to the root, may decrease the value of root hairs for P acquisition in high-strength, high-P soils. Nevertheless, this work demonstrates that root hairs are a valuable trait for plant growth and nutrient acquisition under combined soil stresses. Selecting plants with superior root hair traits is important for improving P uptake efficiency and hence the sustainability of agricultural systems.

Anti-Inflammatory Effects of Vitis thunbergii var. taiwaniana on Knee Damage Associated with Arthritis

PubMed Central

Tsai, Ching-Fent; Wang, Kun-Teng; Chen, Lih-Geeng; Lee, Chia-Jung; Tseng, Sung-Hui

2014-01-01

Abstract Vitis thunbergii Sieb. et Zucc. var. taiwaniana Lu (VT) is an indigenous plant in Taiwan that is traditionally used for promoting joint health. In this study, we used in vitro primary human chondrocytes (PHCs) and two in vivo animal models to evaluate the anti-inflammatory effects of VT on arthritis. Results showed that the water extract of the stems and roots from VT (VT-SR) was rich in flavones and phenols with 1.1 mg/g of resveratrol, 6.7 mg/g of hopeaphenol, and 5.1 mg/g of (+)-ɛ-viniferin. VT-SR significantly scavenged DPPH radicals and inhibited prostaglandin E2 (PGE2) production in lipopolysaccharide (LPS)-induced PHCs without exhibiting significant cytotoxicity. In in vivo models, the VT-SR (500 mg/kg) significantly decreased serum PGE2 and knee 2-18F-fluoro-2-deoxy-D-glucose (18F-FDG) levels in LPS-induced acute inflammatory arthritis in rabbits. In addition, dietary supplementation with VT-SR for 28 days significantly alleviated type II collagenase-induced rat osteoarthritis with improvements in weight bearing and range of motion tests. In conclusion, our results suggest that the VT-SR is a good candidate for developing dietary supplements to prevent joint deterioration and inhibit inflammation. PMID:24720858

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

Communities of arbuscular mycorrhizal fungi in Pyrus pyrifolia var. culta (Japanese pear) and an understory herbaceous plant Plantago asiatica.

PubMed

Yoshimura, Yuko; Ido, Akifumi; Matsumoto, Teruyuki; Yamato, Masahide

2013-01-01

We investigated communities of arbuscular mycorrhizal fungi (AMF) in the fine roots of Pyrus pyrifolia var. culta, and Plantago asiatica to consider the relationship between orchard trees and herbaceous plants in AMF symbioses. The AMF communities were analyzed on the basis of the partial fungal DNA sequences of the nuclear small subunit ribosomal RNA gene (SSU rDNA), which were amplified using the AMF-specific primers AML1 and AML2. Phylogenetic analysis showed that the obtained AMF sequences were divided into 23 phylotypes. Among them, 12 phylotypes included AMF from both host plants, and most of the obtained sequences (689/811) were affiliated to them. Canonical correspondence analysis showed that the host plant species did not have a significant effect on the distribution of AMF phylotypes, whereas the effects of sampling site, soil total C, soil total N and soil-available P were significant. It was also found that the mean observed overlaps of AMF phylotypes between the paired host plants in the same soil cores (27.1% of phylotypes shared) were significantly higher than the mean 1,000 simulated overlaps (14.2%). Furthermore, the same AMF sequences (100% sequence identity) were detected from both host plants in 8/12 soil cores having both roots. Accordingly, we concluded that Py. pyrifolia and Pl. asiatica examined shared some AMF communities, which suggested that understory herbaceous plants may function as AMF inoculum sources for orchard trees.

Communities of Arbuscular Mycorrhizal Fungi in Pyrus pyrifolia var. culta (Japanese pear) and an Understory Herbaceous Plant Plantago asiatica

PubMed Central

Yoshimura, Yuko; Ido, Akifumi; Matsumoto, Teruyuki; Yamato, Masahide

2013-01-01

We investigated communities of arbuscular mycorrhizal fungi (AMF) in the fine roots of Pyrus pyrifolia var. culta, and Plantago asiatica to consider the relationship between orchard trees and herbaceous plants in AMF symbioses. The AMF communities were analyzed on the basis of the partial fungal DNA sequences of the nuclear small subunit ribosomal RNA gene (SSU rDNA), which were amplified using the AMF-specific primers AML1 and AML2. Phylogenetic analysis showed that the obtained AMF sequences were divided into 23 phylotypes. Among them, 12 phylotypes included AMF from both host plants, and most of the obtained sequences (689/811) were affiliated to them. Canonical correspondence analysis showed that the host plant species did not have a significant effect on the distribution of AMF phylotypes, whereas the effects of sampling site, soil total C, soil total N and soil-available P were significant. It was also found that the mean observed overlaps of AMF phylotypes between the paired host plants in the same soil cores (27.1% of phylotypes shared) were significantly higher than the mean 1,000 simulated overlaps (14.2%). Furthermore, the same AMF sequences (100% sequence identity) were detected from both host plants in 8/12 soil cores having both roots. Accordingly, we concluded that Py. pyrifolia and Pl. asiatica examined shared some AMF communities, which suggested that understory herbaceous plants may function as AMF inoculum sources for orchard trees. PMID:23614902

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.

Effects of aluminum on nucleoli in root tip cells and selected physiological and biochemical characters in Allium cepa var. agrogarum L

PubMed Central

2010-01-01

Background Increased Al concentration causes reduction of mitotic activity, induction of nucleolar alteration, increase of the production of ROS and alteration of several antioxidant enzyme activities in plant cells. Allium cepa is an excellent plant and a useful biomarker for environmental monitoring. Limited information is available about the effects of Al on nucleoli, antioxidant enzyme system, contents of MDA and soluble protein in A. cepa. Therefore, we carried out the investigation in order to better understand the effects of Al on the growth, nucleoli in root tip cells and selected physiological and biochemical characters. Results The results showed that the root growth exposed to 50 μM Al was inhibited significantly. 50 μM Al could induce some particles of argyrophilic proteins scattered in the nuclei and extruded from the nucleoli into the cytoplasm. The nucleolus did not disaggregate normally and still remained its characteristic structure during metaphase. Nucleolar reconstruction was inhibited. 50 μM Al induced high activities of SOD and POD in leaves and roots significantly (P < 0.05) when compared with control, whereas the level of CAT was low significantly (P < 0.05). At 50 μM Al the content of MDA in leaves was high significantly (P < 0.05) at 9th day and in roots increased (P < 0.05) with prolonging the treatment time during 6-12 days. The soluble protein content in leaves treated with 50 μM Al was high significantly (P < 0.05) at 6th day and increased with prolonging the treatment time. Conclusions We suggest that variations in nucleoli and the alterations of antioxidant enzyme activities, MDA and soluble protein contents in Allium cepa can serve as useful biomarkers, which can provide valuable information for monitoring and forecasting effects of exposure to Al in real scenarios conditions. Among the antioxidant enzymes SOD and POD appear to play a key role in the antioxidant defense mechanism under Al toxicity condition. Data from MDA

Effects of aluminum on nucleoli in root tip cells and selected physiological and biochemical characters in Allium cepa var. agrogarum L.

PubMed

Qin, Rong; Jiao, Yunqiu; Zhang, Shanshan; Jiang, Wusheng; Liu, Donghua

2010-10-21

Increased Al concentration causes reduction of mitotic activity, induction of nucleolar alteration, increase of the production of ROS and alteration of several antioxidant enzyme activities in plant cells. Allium cepa is an excellent plant and a useful biomarker for environmental monitoring. Limited information is available about the effects of Al on nucleoli, antioxidant enzyme system, contents of MDA and soluble protein in A. cepa. Therefore, we carried out the investigation in order to better understand the effects of Al on the growth, nucleoli in root tip cells and selected physiological and biochemical characters. The results showed that the root growth exposed to 50 μM Al was inhibited significantly. 50 μM Al could induce some particles of argyrophilic proteins scattered in the nuclei and extruded from the nucleoli into the cytoplasm. The nucleolus did not disaggregate normally and still remained its characteristic structure during metaphase. Nucleolar reconstruction was inhibited. 50 μM Al induced high activities of SOD and POD in leaves and roots significantly (P < 0.05) when compared with control, whereas the level of CAT was low significantly (P < 0.05). At 50 μM Al the content of MDA in leaves was high significantly (P < 0.05) at 9(th) day and in roots increased (P < 0.05) with prolonging the treatment time during 6-12 days. The soluble protein content in leaves treated with 50 μM Al was high significantly (P < 0.05) at 6(th) day and increased with prolonging the treatment time. We suggest that variations in nucleoli and the alterations of antioxidant enzyme activities, MDA and soluble protein contents in Allium cepa can serve as useful biomarkers, which can provide valuable information for monitoring and forecasting effects of exposure to Al in real scenarios conditions. Among the antioxidant enzymes SOD and POD appear to play a key role in the antioxidant defense mechanism under Al toxicity condition. Data from MDA concentration show that Al

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.

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.

Root growth, secondary root formation and root gravitropism in carotenoid-deficient seedlings of Zea mays L

NASA Technical Reports Server (NTRS)

Ng, Y. K.; Moore, R.

1985-01-01

The effect of ABA on root growth, secondary-root formation and root gravitropism in seedlings of Zea mays was investigated by using Fluridone-treated seedlings and a viviparous mutant, both of which lack carotenoids and ABA. Primary roots of seedlings grown in the presence of Fluridone grew significantly slower than those of control (i.e. untreated) roots. Elongation of Fluridone-treated roots was inhibited significantly by the exogenous application of 1 mM ABA. Exogenous application of 1 micromole and 1 nmole ABA had either no effect or only a slight stimulatory effect on root elongation, depending on the method of application. The absence of ABA in Fluridone-treated plants was not an important factor in secondary-root formation in seedlings less than 9-10 d old. However, ABA may suppress secondary-root formation in older seedlings, since 11-d-old control seedlings had significantly fewer secondary roots than Fluridone-treated seedlings. Roots of Fluridone-treated and control seedlings were graviresponsive. Similar data were obtained for vp-9 mutants of Z. mays, which are phenotypically identical to Fluridone-treated seedlings. These results indicate that ABA is necessary for neither secondary-root formation nor for positive gravitropism by primary roots.

AFLP analysis of Cynodon dactylon (L.) Pers. var. dactylon genetic variation.

PubMed

Wu, Y Q; Taliaferro, C M; Bai, G H; Anderson, M P

2004-08-01

Cynodon dactylon (L.) Pers. var. dactylon (common bermudagrass) is geographically widely distributed between about lat 45 degrees N and lat 45 degrees S, penetrating to about lat 53 degrees N in Europe. The extensive variation of morphological and adaptive characteristics of the taxon is substantially documented, but information is lacking on DNA molecular variation in geographically disparate forms. Accordingly, this study was conducted to assess molecular genetic variation and genetic relatedness among 28 C. dactylon var. dactylon accessions originating from 11 countries on 4 continents (Africa, Asia, Australia, and Europe). A fluorescence-labeled amplified fragment length polymorphism (AFLP) DNA profiling method was used to detect the genetic diversity and relatedness. On the basis of 443 polymorphic AFLP fragments from 8 primer combinations, the accessions were grouped into clusters and subclusters associating with their geographic origins. Genetic similarity coefficients (SC) for the 28 accessions ranged from 0.53 to 0.98. Accessions originating from Africa, Australia, Asia, and Europe formed major groupings as indicated by cluster and principal coordinate analysis. Accessions from Australia and Asia, though separately clustered, were relatively closely related and most distantly related to accessions of European origin. African accessions formed two distant clusters and had the greatest variation in genetic relatedness relative to accessions from other geographic regions. Sampling the full extent of genetic variation in C. dactylon var. dactylon would require extensive germplasm collection in the major geographic regions of its distributional range.

Effects of GA3 Pregerminative Treatment on Gentiana lutea L. var. aurantiaca Germination and Seedlings Morphology

PubMed Central

González-López, Óscar; Casquero, Pedro A.

2014-01-01

Gentiana lutea L. is widely used in bitter beverages and in medicine; Gentianae Radix is the pharmaceutical name of the root of G. lutea. These uses have generated a high demand. The wild populations of Gentiana lutea var. aurantiaca (M. Laínz) M. Laínz have been decimated; it is necessary to establish guidelines for its cultivation. Gentian as most alpine species has dormant seeds. Dormancy can be removed by cold and by means of a gibberellic acid (GA3) treatment. However, cold treatments produce low germination percentages and GA3 treatments may produce off-type seedlings. So, the objective was to determine, for the first time, the presowing treatments that allow high germination rate and good seedling morphology. The best pregerminative doses of GA3 to break seed dormancy were 100, 500, and 1000 ppm, while the best doses to optimize the seedling habit were 50 and 100 ppm. This study provides, for the first time, a 100 ppm GA3 dose that led to a high germination rate and good seedling morphology, as the starting point for gentian regular cultivation. PMID:25105167

Effects of GA3 pregerminative treatment on Gentiana lutea L. var. aurantiaca germination and seedlings morphology.

PubMed

González-López, Óscar; Casquero, Pedro A

2014-01-01

Gentiana lutea L. is widely used in bitter beverages and in medicine; Gentianae Radix is the pharmaceutical name of the root of G. lutea. These uses have generated a high demand. The wild populations of Gentiana lutea var. aurantiaca (M. Laínz) M. Laínz have been decimated; it is necessary to establish guidelines for its cultivation. Gentian as most alpine species has dormant seeds. Dormancy can be removed by cold and by means of a gibberellic acid (GA3) treatment. However, cold treatments produce low germination percentages and GA3 treatments may produce off-type seedlings. So, the objective was to determine, for the first time, the presowing treatments that allow high germination rate and good seedling morphology. The best pregerminative doses of GA3 to break seed dormancy were 100, 500, and 1000 ppm, while the best doses to optimize the seedling habit were 50 and 100 ppm. This study provides, for the first time, a 100 ppm GA3 dose that led to a high germination rate and good seedling morphology, as the starting point for gentian regular cultivation.

Occurrence and Distribution of Proteinase of Streptococcus faecalis var. liquefaciens1

PubMed Central

Shugart, Lee R.; Beck, Raymond W.

1966-01-01

Shugart, Lee R. (University of Tennessee, Knoxville), and Raymond W. Beck. Occurrence and distribution of proteinase of Streptococcus faecalis var. liquefaciens. J. Bacteriol. 92:338–341. 1966.—The proteolytic enzyme produced by Streptococcus faecalis var. liquefaciens (ATCC 13398) was shown to be an exoenzyme. The production of the proteinase was followed in growing cultures, and its distribution was compared with that of the intracellular enzymes reduced nicotinamide adenine dinucleotide (NADH2) peroxidase and lactate dehydrogenase. The proteinase appeared in the culture medium prior to the stationary phase of growth, whereas the other enzymes could be found only in whole cells. Fractionation of whole cells by sonic treatment and by treatment with lysozyme showed the proteinase to be associated primarily with the cell wall and cell membrane, and NADH2 peroxidase to be associated only with the cytoplasmic fractions. PMID:16562116

Root decisions.

PubMed

Hodge, Angela

2009-06-01

Root systems have recognizable developmental plans when grown in solution or agar; however, these plans often must be modified to cope with the prevailing conditions in the soil environment such as the avoidance of obstacles and the exploitation of nutrient-rich patches or water zones. The modular structure of roots enables them to respond to their environment, and roots are very adaptive at modifying growth throughout the root system to concentrate their efforts in the areas that are the most profitable. Roots also form associations with microorganisms as a strategy to enhance resource capture. However, while the responses of roots in nutrient patches are well-recognized, overall 'rules of response' and variation in strategy among plant species that can be applied in a number of different environments are still lacking. Finally, there is increasing evidence that root-root interactions are much more sophisticated than previously thought, and the evidence for roots to identify self from non-self roots will be briefly discussed.

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.

Inhibition of nitrate transport by anti-nitrate reductase IgG fragments and the identification of plasma membrane associated nitrate reductase in roots of barley seedlings

NASA Technical Reports Server (NTRS)

Ward, M. R.; Tischner, R.; Huffaker, R. C.

1988-01-01

Membrane associated nitrate reductase (NR) was detected in plasma membrane (PM) fractions isolated by aqueous two-phase partitioning from barley (Hordeum vulgare L. var CM 72) roots. The PM associated NR was not removed by washing vesicles with 500 millimolar NaCl and 1 millimolar EDTA and represented up to 4% of the total root NR activity. PM associated NR was stimulated up to 20-fold by Triton X-100 whereas soluble NR was only increased 1.7-fold. The latency was a function of the solubilization of NR from the membrane. NR, solubilized from the PM fraction by Triton X-100 was inactivated by antiserum to Chlorella sorokiniana NR. Anti-NR immunoglobulin G fragments purified from the anti-NR serum inhibited NO3- uptake by more than 90% but had no effect on NO2- uptake. The inhibitory effect was only partially reversible; uptake recovered to 50% of the control after thorough rinsing of roots. Preimmune serum immunoglobulin G fragments inhibited NO3- uptake 36% but the effect was completely reversible by rinsing. Intact NR antiserum had no effect on NO3- uptake. The results present the possibility that NO3- uptake and NO3- reduction in the PM of barley roots may be related.

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

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.

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.

Root hairs increase root exudation and rhizosphere extension

NASA Astrophysics Data System (ADS)

Holz, Maire; Zarebandanadkouki, Mohsen; Kuzyakov, Yakov; Carmintati, Andrea

2017-04-01

Plant roots employ various mechanisms to increase their access to limited soil resources. An example of such strategies is the production of root hairs. Root hairs extend the root surface and therefore increase the access to nutrients. Additionally, carbon release from root hairs might facilitate nutrient uptake by spreading of carbon in the rhizosphere and enhancing microbial activity. The aim of this study was to test: i) how root hairs change the allocation of carbon in the soil-plant system; ii) whether root hairs exude carbon into the soil and iii) how differences in C release between plants with and without root hairs affect rhizosphere extension. We grew barley plants with and without root hairs (wild type: WT, bald root barley: brb) in rhizoboxes filled with a sandy soil. Root elongation was monitored over time. After 4 weeks of growth, plants were labelled with 14CO2. A filter paper was placed on the soil surface before labelling and was removed after 36 h. 14C imaging of the soil surface and of the filter paper was used to quantify the allocation of 14C into the roots and the exudation of 14C, respectively. Plants were sampled destructively one day after labeling to quantify 14C in the plant-soil system. 14CO2 release from soil over time (17 d) was quantified by trapping CO2 in NaOH with an additional subset of plants. WT and brb plants had a similar aboveground biomass and allocated similar amounts of 14C into shoots (170 KBq for WT; 152 KBq for brb) and roots one day after labelling. Biomass of root, rhizosphere soil as well as root elongation were lower for brb compared to the wild type. WT plants transported more C from the shoots to the roots (22.8% for WT; 13.8% for brb) and from the root into the rhizosphere (8.8% for WT 3.5% for brb). Yet lower amounts of 14CO2 were released from soil over time for WT. Radial and longitudinal rhizosphere extension was increased for WT compared to brb (4.7 vs. 2.6 mm; 5.6 vs. 3.1 cm). The total exudation which was

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.

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.

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.

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.

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.

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.

Variability of chemical composition and antioxidant activity of essential oils between Myrtus communis var. Leucocarpa DC and var. Melanocarpa DC.

PubMed

Petretto, Giacomo Luigi; Maldini, Mariateresa; Addis, Roberta; Chessa, Mario; Foddai, Marzia; Rourke, Jonathan P; Pintore, Giorgio

2016-04-15

Essential oils (EOs) from several individuals of Myrtus communis L. (M. communis) growing in different habitats in Sardinia have been studied. The analyses were focused on four groups of samples, namely cultivated and wild M. communis var. melanocarpa DC, characterized by red/purple berries, and cultivated and wild M. communis var. leucocarpa DC, characterized by white berries. Qualitative and quantitative analyses demonstrated different EO fingerprints among the studied samples: cultivated and wild leucocarpa variety differs mainly from the melanocarpa variety by a high amount of myrtenyl acetate (>200 mg/mL and 0.4 mg/mL in leucocarpa and melanocarpa varieties respectively). Conversely, the wild group is characterized by a higher amount, compared with the cultivated species, of linalool (about 110 mg/mL and 20 mg/mL respectively), linalyl acetate (about 24 mg/mL and about 6 mg/mL respectively) whereas EOs of the cultivated plants were rich in pinocarveol-cis compared with wild plants (about 2 mg/mL and about 0.5 mg/mL respectively). Principal component analysis applied to the chromatographic data confirm a differentiation and classification of EOs from the four groups of M. communis plants. Finally, antioxidant activity of the studied EOs shows differences between the various categories of samples. Copyright © 2015 Elsevier Ltd. All rights reserved.

Wheat bran soil inoculant of sumateran nematode-trapping fungi as biocontrol agents of the root-knot nematode meloidogyne incognita on deli tobacco (nicotiana tabaccum l) cv. deli 4

NASA Astrophysics Data System (ADS)

Dwi Sri Hastuti, Liana; Faull, Jane

2018-03-01

A pot experiment was carried out to test the effectiveness of nematode-trapping fungi (NTF) isolated from Sumatera for controlling infection by the root-knot nematode (RKN) on Deli tobacco plant. Wheat bran soil containing 109 conidia of Arthrobotrys. oligospora, Candellabrella musiformis and Dactylella eudermata was added to the soil as a dry inoculum. Carbofuran was also applied as chemical agent and comparison treatment. Seedling tobacco (Nicotiana tabacum L.) cv. Deli 4 was inoculated with root knot (Meloidogyne incognita Chitwood.) seven days after the plant were transplanted to the pots. A. oligospora, C. musiformis and D. eudermata were found to be reliable as biocontrol agents, reducing the number of vermiform nematodes, swollen root, sausage shaped and galls in tobacco plant after 7, 15 and 30 days of infection with M. incognita. Treatment with NTF produced results that were comparable with Carbofuran® as a control agent in the reduction of the number of infections in tobacco plant caused by M. incognita in Nicotiana tabacum var. Deli 4. They also optimize the growth of the tobacco plants especially up to 15 days after infection.

Root development during soil genesis: effects of root-root interactions, mycorrhizae, and substrate

NASA Astrophysics Data System (ADS)

Salinas, A.; Zaharescu, D. G.

2015-12-01

A major driver of soil formation is the colonization and transformation of rock by plants and associated microbiota. In turn, substrate chemical composition can also influence the capacity for plant colonization and development. In order to better define these relationships, a mesocosm study was set up to analyze the effect mycorrhizal fungi, plant density and rock have on root development, and to determine the effect of root morphology on weathering and soil formation. We hypothesized that plant-plant and plant-fungi interactions have a stronger influence on root architecture and rock weathering than the substrate composition alone. Buffalo grass (Bouteloua dactyloides) was grown in a controlled environment in columns filled with either granular granite, schist, rhyolite or basalt. Each substrate was given two different treatments, including grass-microbes and grass-microbes-mycorrhizae and incubated for 120, 240, and 480 days. Columns were then extracted and analyzed for root morphology, fine fraction, and pore water major element content. Preliminary results showed that plants produced more biomass in rhyolite, followed by schist, basalt, and granite, indicating that substrate composition is an important driver of root development. In support of our hypothesis, mycorrhizae was a strong driver of root development by stimulating length growth, biomass production, and branching. However, average root length and branching also appeared to decrease in response to high plant density, though this trend was only present among roots with mycorrhizal fungi. Interestingly, fine fraction production was negatively correlated with average root thickness and volume. There is also slight evidence indicating that fine fraction production is more related to substrate composition than root morphology, though this data needs to be further analyzed. Our hope is that the results of this study can one day be applied to agricultural research in order to promote the production of crops

Efficient in vitro propagation of Artemisia nilagirica var. nilagirica (Indian wormwood) and assessment of genetic fidelity of micropropagated plants.

PubMed

Shinde, Smita; Sebastian, Joseph Kadanthottu; Jain, Jyothi Ramesh; Hanamanthagouda, Manohar Shirugumbi; Murthy, Hosakatte Niranjana

2016-10-01

A reliable protocol has been established for in vitro propagation of Artemisia nilagirica var. nilagirica (Indian wormwood), a valuable medicinal plant from India. A highly proliferating organogenic callus was obtained on Murashige and Skoog (MS) medium supplemented with 2.5 µM IAA when nodal explants were cultured on MS medium supplemented with various growth regulators. Further, highest regeneration frequency (83.3 %) of adventitious shoots was observed, when the callus was sub-cultured on MS medium supplemented with 6-benzylaminopurine (BAP; 2.5 µM) along with 7.5 µM 2-isopentenyl adenine (2-iP). An optimal of 10.16 ± 2.24 shoots were regenerated on medium supplemented with 2.5 µM BAP + 7.5 µM 2-iP. Quarter strength MS medium supplemented with 10 µM IBA was effective for rooting of the shoots. Ex-vitro plants were normal and were established successfully. Cytological and molecular marker studies showed that regenerated plants showed genetic stability in micro-propagated plants.

Experimental reintroduction of the federally endangered Santa Cruz Island bush mallow (Malacothamnus fasciculatus var. nestioticus)

USGS Publications Warehouse

Wilken, D.H.; McEachern, K.

2011-01-01

Studies of Malacothamnus fasciculatus var. nesioticus were begun in 1995 to understand its distribution, reproductive biology and ecological requirements. After 100+ years of depredation by sheep, two known populations of fewer than 20 plants each survived in 1995. Molecular studies showed that each of the two populations was composed of 1–3 genets. During our study, two additional populations of similar size were discovered. Plants are self-compatible but require insect visitation to augment pollination. Based on seed set, viable embryos, and germination rates, we found no evidence for inbreeding depression. Bush mallow also reproduces vegetatively by rhizomes, the primary means of establishment and persistence in natural populations, and a key feature for maximizing recovery success. Ex situ observations and trial in situ outplantings suggested that supplemental watering was critical to initial survival. We developed a recovery strategy composed of four plots located at varying elevations and aspects. Each plot was enclosed to exclude feral pigs, which posed a continuing threat. Each plot was planted with twelve rooted plants derived from each of three natural populations. Plants were provided supplemental watering for four months. Survivorship after one year ranged from 46% to 91%. Significant differences in survivorship were observed relative to source of plants. After twelve months some plants were flowering and reproducing vegetatively.

Rooting gene trees without outgroups: EP rooting.

PubMed

Sinsheimer, Janet S; Little, Roderick J A; Lake, James A

2012-01-01

Gene sequences are routinely used to determine the topologies of unrooted phylogenetic trees, but many of the most important questions in evolution require knowing both the topologies and the roots of trees. However, general algorithms for calculating rooted trees from gene and genomic sequences in the absence of gene paralogs are few. Using the principles of evolutionary parsimony (EP) (Lake JA. 1987a. A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. Mol Biol Evol. 4:167-181) and its extensions (Cavender, J. 1989. Mechanized derivation of linear invariants. Mol Biol Evol. 6:301-316; Nguyen T, Speed TP. 1992. A derivation of all linear invariants for a nonbalanced transversion model. J Mol Evol. 35:60-76), we explicitly enumerate all linear invariants that solely contain rooting information and derive algorithms for rooting gene trees directly from gene and genomic sequences. These new EP linear rooting invariants allow one to determine rooted trees, even in the complete absence of outgroups and gene paralogs. EP rooting invariants are explicitly derived for three taxon trees, and rules for their extension to four or more taxa are provided. The method is demonstrated using 18S ribosomal DNA to illustrate how the new animal phylogeny (Aguinaldo AMA et al. 1997. Evidence for a clade of nematodes, arthropods, and other moulting animals. Nature 387:489-493; Lake JA. 1990. Origin of the metazoa. Proc Natl Acad Sci USA 87:763-766) may be rooted directly from sequences, even when they are short and paralogs are unavailable. These results are consistent with the current root (Philippe H et al. 2011. Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature 470:255-260).

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...

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.

RootJS: Node.js Bindings for ROOT 6

NASA Astrophysics Data System (ADS)

Beffart, Theo; Früh, Maximilian; Haas, Christoph; Rajgopal, Sachin; Schwabe, Jonas; Wolff, Christoph; Szuba, Marek

2017-10-01

We present rootJS, an interface making it possible to seamlessly integrate ROOT 6 into applications written for Node.js, the JavaScript runtime platform increasingly commonly used to create high-performance Web applications. ROOT features can be called both directly from Node.js code and by JIT-compiling C++ macros. All rootJS methods are invoked asynchronously and support callback functions, allowing non-blocking operation of Node.js applications using them. Last but not least, our bindings have been designed to platform-independent and should therefore work on all systems supporting both ROOT 6 and Node.js. Thanks to rootJS it is now possible to create ROOT-aware Web applications taking full advantage of the high performance and extensive capabilities of Node.js. Examples include platforms for the quality assurance of acquired, reconstructed or simulated data, book-keeping and e-log systems, and even Web browser-based data visualisation and analysis.

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.

New Records of Mosquitoes (Diptera: Culicidae) from Bolívar State in South Eastern Venezuela, with 27 New Species for the State and 5 of Them New in the Country

PubMed Central

Berti, Jesús; Guzmán, Hernán; Estrada, Yarys; Ramírez, Rodrigo

2015-01-01

This is the first part of a series of studies related to mosquito ecological and biogeographic aspects. A total of 69 mosquito species (Diptera: Culicidae) was collected in 16 localities sampled in the Gran Sabana Municipality, Canaima National Park, and Venezuela. Twenty-seven mosquito species are recorded for the first time from Bolívar State, Venezuela. Five of them species are reported for the first time in Venezuela: Anopheles malefactor Dyar and Knab (1907); Chagasia bonneae Root (1927); Chagasia ablusa Harbach (2009); Culex anduzei Lane (1944), and Uranotaenia leucoptera Theobald (1907). Their medical importance is commented, and ecological and epidemiological aspects are discussed. A checklist of the mosquito species reported in the Gran Sabana County is given. PMID:25853113

Compensatory Root Water Uptake of Overlapping Root Systems

NASA Astrophysics Data System (ADS)

Agee, E.; Ivanov, V. Y.; He, L.; Bisht, G.; Shahbaz, P.; Fatichi, S.; Gough, C. M.; Couvreur, V.; Matheny, A. M.; Bohrer, G.

2015-12-01

Land-surface models use simplified representations of root water uptake based on biomass distributions and empirical functions that constrain water uptake during unfavorable soil moisture conditions. These models fail to capture the observed hydraulic plasticity that allows plants to regulate root hydraulic conductivity and zones of active uptake based on local gradients. Recent developments in root water uptake modeling have sought to increase its mechanistic representation by bridging the gap between physically based microscopic models and computationally feasible macroscopic approaches. It remains to be demonstrated whether bulk parameterization of microscale characteristics (e.g., root system morphology and root conductivity) can improve process representation at the ecosystem scale. We employ the Couvreur method of microscopic uptake to yield macroscopic representation in a coupled soil-root model. Using a modified version of the PFLOTRAN model, which represents the 3-D physics of variably saturated soil, we model a one-hectare temperate forest stand under natural and synthetic climatic forcing. Our results show that as shallow soil layers dry, uptake at the tree and stand level shift to deeper soil layers, allowing the transpiration stream demanded by the atmosphere. We assess the potential capacity of the model to capture compensatory root water uptake. Further, the hydraulic plasticity of the root system is demonstrated by the quick response of uptake to rainfall pulses. These initial results indicate a promising direction for land surface models in which significant three-dimensional information from large root systems can be feasibly integrated into the forest scale simulations of root water uptake.

Root proliferation in decaying roots and old root channels: A nutrient conservation mechanism in oligotrophic mangrove forests?

USGS Publications Warehouse

McKee, K.L.

2001-01-01

1. In oligotrophic habitats, proliferation of roots in nutrient-rich microsites may contribute to overall nutrient conservation by plants. Peat-based soils on mangrove islands in Belize are characterized by the presence of decaying roots and numerous old root channels (0.1-3.5 cm diameter) that become filled with living and highly branched roots of Rhizophora mangle and Avicennia germinans. The objectives of this study were to quantify the proliferation of roots in these microsites and to determine what causes this response. 2. Channels formed by the refractory remains of mangrove roots accounted for only 1-2% of total soil volume, but the proportion of roots found within channels varied from 9 to 24% of total live mass. Successive generations of roots growing inside increasingly smaller root channels were also found. 3. When artificial channels constructed of PVC pipe were buried in the peat for 2 years, those filled with nutrient-rich organic matter had six times more roots than empty or sand-filled channels, indicating a response to greater nutrient availability rather than to greater space or less impedance to root growth. 4. Root proliferation inside decaying roots may improve recovery of nutrients released from decomposing tissues before they can be leached or immobilized in this intertidal environment. Greatest root proliferation in channels occurred in interior forest zones characterized by greater soil waterlogging, which suggests that this may be a strategy for nutrient capture that minimizes oxygen losses from the whole root system. 5. Improved efficiency of nutrient acquisition at the individual plant level has implications for nutrient economy at the ecosystem level and may explain, in part, how mangroves persist and grow in nutrient-poor environments.

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

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.

Rooting Gene Trees without Outgroups: EP Rooting

PubMed Central

Sinsheimer, Janet S.; Little, Roderick J. A.; Lake, James A.

2012-01-01

Gene sequences are routinely used to determine the topologies of unrooted phylogenetic trees, but many of the most important questions in evolution require knowing both the topologies and the roots of trees. However, general algorithms for calculating rooted trees from gene and genomic sequences in the absence of gene paralogs are few. Using the principles of evolutionary parsimony (EP) (Lake JA. 1987a. A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. Mol Biol Evol. 4:167–181) and its extensions (Cavender, J. 1989. Mechanized derivation of linear invariants. Mol Biol Evol. 6:301–316; Nguyen T, Speed TP. 1992. A derivation of all linear invariants for a nonbalanced transversion model. J Mol Evol. 35:60–76), we explicitly enumerate all linear invariants that solely contain rooting information and derive algorithms for rooting gene trees directly from gene and genomic sequences. These new EP linear rooting invariants allow one to determine rooted trees, even in the complete absence of outgroups and gene paralogs. EP rooting invariants are explicitly derived for three taxon trees, and rules for their extension to four or more taxa are provided. The method is demonstrated using 18S ribosomal DNA to illustrate how the new animal phylogeny (Aguinaldo AMA et al. 1997. Evidence for a clade of nematodes, arthropods, and other moulting animals. Nature 387:489–493; Lake JA. 1990. Origin of the metazoa. Proc Natl Acad Sci USA 87:763–766) may be rooted directly from sequences, even when they are short and paralogs are unavailable. These results are consistent with the current root (Philippe H et al. 2011. Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature 470:255–260). PMID:22593551

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

Root Hairs

PubMed Central

Grierson, Claire; Nielsen, Erik; Ketelaarc, Tijs; Schiefelbein, John

2014-01-01

Roots hairs are cylindrical extensions of root epidermal cells that are important for acquisition of nutrients, microbe interactions, and plant anchorage. The molecular mechanisms involved in the specification, differentiation, and physiology of root hairs in Arabidopsis are reviewed here. Root hair specification in Arabidopsis is determined by position-dependent signaling and molecular feedback loops causing differential accumulation of a WD-bHLH-Myb transcriptional complex. The initiation of root hairs is dependent on the RHD6 bHLH gene family and auxin to define the site of outgrowth. Root hair elongation relies on polarized cell expansion at the growing tip, which involves multiple integrated processes including cell secretion, endomembrane trafficking, cytoskeletal organization, and cell wall modifications. The study of root hair biology in Arabidopsis has provided a model cell type for insights into many aspects of plant development and cell biology. PMID:24982600

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.

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.

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...

AmeriFlux US-Var Vaira Ranch- Ione

DOE Data Explorer

Baldocchi, Dennis [University of California, Berkeley

2016-01-01

This is the AmeriFlux version of the carbon flux data for the site US-Var Vaira Ranch- Ione. Site Description - Located in the lower foothills of the Sierra Nevada Mountains on privately owned land, the Vaira Ranch site is classified as a grassland dominated by C3 annual grasses. Managed by local rancher, Fran Vaira, brush has been periodically removed for cattle grazing. Species include a variety of grasses and herbs, including purple false brome, smooth cat's ear, and rose clover. Growing season is confined to the wet season only, typically from October to early May.

Descendant root volume varies as a function of root type: estimation of root biomass lost during uprooting in Pinus pinaster.

PubMed

Danjon, Frédéric; Caplan, Joshua S; Fortin, Mathieu; Meredieu, Céline

2013-01-01

Root systems of woody plants generally display a strong relationship between the cross-sectional area or cross-sectional diameter (CSD) of a root and the dry weight of biomass (DWd) or root volume (Vd) that has grown (i.e., is descendent) from a point. Specification of this relationship allows one to quantify root architectural patterns and estimate the amount of material lost when root systems are extracted from the soil. However, specifications of this relationship generally do not account for the fact that root systems are comprised of multiple types of roots. We assessed whether the relationship between CSD and Vd varies as a function of root type. Additionally, we sought to identify a more accurate and time-efficient method for estimating missing root volume than is currently available. We used a database that described the 3D root architecture of Pinus pinaster root systems (5, 12, or 19 years) from a stand in southwest France. We determined the relationship between CSD and Vd for 10,000 root segments from intact root branches. Models were specified that did and did not account for root type. The relationships were then applied to the diameters of 11,000 broken root ends to estimate the volume of missing roots. CSD was nearly linearly related to the square root of Vd, but the slope of the curve varied greatly as a function of root type. Sinkers and deep roots tapered rapidly, as they were limited by available soil depth. Distal shallow roots tapered gradually, as they were less limited spatially. We estimated that younger trees lost an average of 17% of root volume when excavated, while older trees lost 4%. Missing volumes were smallest in the central parts of root systems and largest in distal shallow roots. The slopes of the curves for each root type are synthetic parameters that account for differentiation due to genetics, soil properties, or mechanical stimuli. Accounting for this differentiation is critical to estimating root loss accurately.

Descendant root volume varies as a function of root type: estimation of root biomass lost during uprooting in Pinus pinaster

PubMed Central

Danjon, Frédéric; Caplan, Joshua S.; Fortin, Mathieu; Meredieu, Céline

2013-01-01

Root systems of woody plants generally display a strong relationship between the cross-sectional area or cross-sectional diameter (CSD) of a root and the dry weight of biomass (DWd) or root volume (Vd) that has grown (i.e., is descendent) from a point. Specification of this relationship allows one to quantify root architectural patterns and estimate the amount of material lost when root systems are extracted from the soil. However, specifications of this relationship generally do not account for the fact that root systems are comprised of multiple types of roots. We assessed whether the relationship between CSD and Vd varies as a function of root type. Additionally, we sought to identify a more accurate and time-efficient method for estimating missing root volume than is currently available. We used a database that described the 3D root architecture of Pinus pinaster root systems (5, 12, or 19 years) from a stand in southwest France. We determined the relationship between CSD and Vd for 10,000 root segments from intact root branches. Models were specified that did and did not account for root type. The relationships were then applied to the diameters of 11,000 broken root ends to estimate the volume of missing roots. CSD was nearly linearly related to the square root of Vd, but the slope of the curve varied greatly as a function of root type. Sinkers and deep roots tapered rapidly, as they were limited by available soil depth. Distal shallow roots tapered gradually, as they were less limited spatially. We estimated that younger trees lost an average of 17% of root volume when excavated, while older trees lost 4%. Missing volumes were smallest in the central parts of root systems and largest in distal shallow roots. The slopes of the curves for each root type are synthetic parameters that account for differentiation due to genetics, soil properties, or mechanical stimuli. Accounting for this differentiation is critical to estimating root loss accurately. PMID

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.

A split-root technique for measuring root water potential.

PubMed

Adeoye, K B; Rawlins, S L

1981-07-01

Water encounters various resistances in moving along a path of decreasing potential energy from the soil through the plant to the atmosphere. The reported relative magnitudes of these pathway resistances vary widely and often these results are conflicting. One reason for such inconsistency is the difficulty in measuring the potential drop across various segments of the soil-plant-atmosphere continuum. The measurement of water potentials at the soil-root interface and in the root xylem of a transpiring plant remains a challenging problem.In the divided root experiment reported here, the measured water potential of an enclosed, nonabsorbing branch of the root system of young corn (Bonanza) plants to infer the water potential of the remaining roots growing in soil was used. The selected root branch of the seedling was grown in a specially constructed Teflon test tube into which a screen-enclosed thermocouple psychrometer was inserted and sealed to monitor the root's water potential. The root and its surrounding atmosphere were assumed to be in vapor equilibrium.

A Split-Root Technique for Measuring Root Water Potential

PubMed Central

Adeoye, Kingsley B.; Rawlins, Stephen L.

1981-01-01

Water encounters various resistances in moving along a path of decreasing potential energy from the soil through the plant to the atmosphere. The reported relative magnitudes of these pathway resistances vary widely and often these results are conflicting. One reason for such inconsistency is the difficulty in measuring the potential drop across various segments of the soil-plant-atmosphere continuum. The measurement of water potentials at the soil-root interface and in the root xylem of a transpiring plant remains a challenging problem. In the divided root experiment reported here, the measured water potential of an enclosed, nonabsorbing branch of the root system of young corn (Bonanza) plants to infer the water potential of the remaining roots growing in soil was used. The selected root branch of the seedling was grown in a specially constructed Teflon test tube into which a screen-enclosed thermocouple psychrometer was inserted and sealed to monitor the root's water potential. The root and its surrounding atmosphere were assumed to be in vapor equilibrium. Images PMID:16661886

Continuous Spectrum LEDs Promote Seedling Quality Traits and Performance of Quercus ithaburensis var. macrolepis

PubMed Central

Smirnakou, Sonia; Ouzounis, Theoharis; Radoglou, Kalliopi M.

2017-01-01

Regulation of the growth, development, and quality of plants by the control of light quality has attracted extensive attention worldwide. The aim of this study was to examine the effects of continuous LED spectrum for indoor plant pre-cultivation and to investigate the morphological and physiological responses of a common broadleaved tree species in Mediterranean environment, Quercus ithaburensis var. macrolepis at seedling developmental stage. Thus, the seedlings were pre-cultivated for 28 days, under five different LED light qualities: (1) Fluorescent (FL) as control light (2) L20AP67 (high in green and moderate in far-red), (3) AP673L (high in green and red), (4) G2 (highest in red and far-red), AP67 (high in blue, red, and far-red), and (5) NS1 (highest in blue and green and lowest in far-red) LEDs. Further examination was held at the nursery for 1 year, on several seedling quality traits. Indeed, AP67 and AP673L triggered higher leaf formation, while L20AP67 positively affected seedling shoot development. NS1 and AP67 LED pre-cultivated seedlings showed significantly higher root fibrosity than those of FL light. Furthermore, NS1 and AP673L LEDs induced fourfold increase on seedling root dry weight than FL light. Hence, evaluating the seedling nursery performance attributes, most of those photomorphogenetic responses previously obtained were still detectable. Even more so, LED pre-cultivated seedlings showed higher survival and faster growth indicating better adaptation even under natural light conditions, a fact further reinforced by the significantly higher Dickson’s quality index acquired. In conclusion, the goal of each nursery management program is the production of high quality seedlings with those desirable traits, which in turn satisfy the specific needs for a particular reforestation site. Thus, the enhanced oak seedling quality traits formed under continuous LEDs spectrum especially of NS1 and AP673L pre-cultivation may potentially fulfill this goal

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

High frequency organogenesis in hypocotyl, cotyledon, leaf and petiole explants of broccoli (Brassica oleracea L. var. italica), an important vegetable crop.

PubMed

Kumar, Pankaj; Srivastava, D K

2015-04-01

Broccoli (Brassica oleracea L. var. italica) is an important, nutritionally rich vegetable crop, but severely affected by environmental stresses, pests and diseases which cause massive yield and quality losses. Genetic manipulation is becoming an important method for broccoli improvement. In the present study, a reproducible and highly efficient protocol for obtaining organogenesis from hypocotyl, cotyledon, leaf and petiole explants of broccoli (Brassica oleracea L. var. italica cv. Solan green head) has been developed. Hypocotyl and cotyledon explants were used from 10 to 12 days old aseptically grown seedlings whereas leaf and petiole explants were excised from 18 to 20 days old green house grown seedlings and surface sterilized. These explants were cultured on shoot induction medium containing different concentration and combination of BAP and NAA. High efficiency shoot regeneration has been achieved in hypocotyl (83.33 %), cotyledon (90.11 %), leaf (62.96 %) and petiole (91.10 %) explants on MS medium supplemented with 3.5 mg/l BAP + 0.019 mg/l NAA 2.5 mg/l BAP + 0.5 mg/l NAA, 4.0 mg/l BAP + 0.5 mg/l NAA and 4.5 mg/l BAP + 0.019 mg/l NAA respectively. Petiole explants showed maximum shoot regeneration response as compared to other explants. MS medium supplemented with 0.10 mg/l NAA was found best for root regeneration (100 %) from in vitro developed shoots. The regenerated complete plantlets were transferred to the pots containing cocopeat and successfully acclimatized. This optimized regeneration protocol can be efficiently used for genetic transformation in broccoli. This is the first comparative report on multiple shoot induction using four different types of explants viz. hypocotyl, cotyledon, leaf and petiole.

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 .

VarBin, a novel method for classifying true and false positive variants in NGS data

PubMed Central

2013-01-01

Background Variant discovery for rare genetic diseases using Illumina genome or exome sequencing involves screening of up to millions of variants to find only the one or few causative variant(s). Sequencing or alignment errors create "false positive" variants, which are often retained in the variant screening process. Methods to remove false positive variants often retain many false positive variants. This report presents VarBin, a method to prioritize variants based on a false positive variant likelihood prediction. Methods VarBin uses the Genome Analysis Toolkit variant calling software to calculate the variant-to-wild type genotype likelihood ratio at each variant change and position divided by read depth. The resulting Phred-scaled, likelihood-ratio by depth (PLRD) was used to segregate variants into 4 Bins with Bin 1 variants most likely true and Bin 4 most likely false positive. PLRD values were calculated for a proband of interest and 41 additional Illumina HiSeq, exome and whole genome samples (proband's family or unrelated samples). At variant sites without apparent sequencing or alignment error, wild type/non-variant calls cluster near -3 PLRD and variant calls typically cluster above 10 PLRD. Sites with systematic variant calling problems (evident by variant quality scores and biases as well as displayed on the iGV viewer) tend to have higher and more variable wild type/non-variant PLRD values. Depending on the separation of a proband's variant PLRD value from the cluster of wild type/non-variant PLRD values for background samples at the same variant change and position, the VarBin method's classification is assigned to each proband variant (Bin 1 to Bin 4). Results To assess VarBin performance, Sanger sequencing was performed on 98 variants in the proband and background samples. True variants were confirmed in 97% of Bin 1 variants, 30% of Bin 2, and 0% of Bin 3/Bin 4. Conclusions These data indicate that VarBin correctly classifies the majority of true

Characterizing pathways by which gravitropic effectors could move from the root cap to the root of primary roots of Zea mays

NASA Technical Reports Server (NTRS)

Moore, R.; McClelen, C. E.

1989-01-01

Plasmodesmata linking the root cap and root in primary roots Zea mays are restricted to approx. 400 protodermal cells bordering approx. 110000 microns2 of the calyptrogen of the root cap. This area is less than 10% of the cross-sectional area of the root-tip at the cap junction. Therefore, gravitropic effectors moving from the root cap to the root can move symplastically only through a relatively small area in the centre of the root. Decapped roots are non-responsive to gravity. However, decapped roots whose caps are replaced immediately after decapping are strongly graviresponsive. Thus, gravicurvature occurs only when the root cap contacts the root, and symplastic continuity between the cap and root is not required for gravicurvature. Completely removing mucilage from the root tip renders the root non-responsive to gravity. Taken together, these data suggest that gravitropic effectors move apoplastically through mucilage from the cap to the root.

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...

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

Root anatomy, morphology, and longevity among root orders in Vaccinium corymbosum (Ericaceae).

PubMed

Valenzuela-Estrada, Luis R; Vera-Caraballo, Vivianette; Ruth, Leah E; Eissenstat, David M

2008-12-01

Understanding root processes at the whole-plant or ecosystem scales requires an accounting of the range of functions within a root system. Studying root traits based on their branching order can be a powerful approach to understanding this complex system. The current study examined the highly branched root system of the ericoid plant, Vaccinium corymbosum L. (highbush blueberry) by classifying its root orders with a modified version of the morphometric approach similar to that used in hydrology for stream classification. Root anatomy provided valuable insight into variation in root function across orders. The more permanent portion of the root system occurred in 4th- and higher-order roots. Roots in these orders had radial growth; the lowest specific root length, N:C ratios, and mycorrhizal colonization; the highest tissue density and vessel number; and the coarsest root diameter. The ephemeral portion of the root system was mainly in the first three root orders. First- and 2nd-order roots were nearly anatomically identical, with similar mycorrhizal colonization and diameter, and also, despite being extremely fine, median lifespans were not very short (115-120 d; estimated with minirhizotrons). Our research underscores the value of examining root traits by root order and its implications to understanding belowground processes.

[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.

Determination of free amino compounds in betalainic fruits and vegetables by gas chromatography with flame ionization and mass spectrometric detection.

PubMed

Kugler, Florian; Graneis, Stephan; Schreiter, Pat P-Y; Stintzing, Florian C; Carle, Reinhold

2006-06-14

Amino acids and amines are the precursors of betalains. Therefore, the profiles of free amino compounds in juices obtained from cactus pears [Opuntia ficus-indica (L.) Mill. cv. Bianca, cv. Gialla, and cv. Rossa], pitaya fruits [Selenicereus megalanthus (K. Schumann ex Vaupel) Moran, Hylocereus polyrhizus (Weber) Britton & Rose, and Hylocereus undatus (Haworth) Britton & Rose], and in extracts from differently colored Swiss chard [Beta vulgaris L. ssp. cicla (L.) Alef. cv. Bright Lights] petioles and red and yellow beets (B. vulgaris L. ssp. vulgaris var. conditiva Alef. cv. Burpee's Golden) were investigated for the first time. Amino compounds were derivatized with propyl chloroformate. While gas chromatography (GC) with mass spectrometry was used for peak assignment, GC flame ionization detection was applied for quantification of individual compounds. Whereas proline was the major free amino compound of cactus pear and pitaya fruit juices, glutamine dominated in Swiss chard stems and beets, respectively. Interestingly, extremely high concentrations of dopamine were detected in Swiss chard stems and beets. Furthermore, the cleavage of betaxanthins caused by derivatization in alkaline reaction solutions is demonstrated for the first time. Amino acids and amines thus released might increase the actual free amino compound contents of the respective sample. To evaluate the contribution of betaxanthin cleavage to total amino acid and amine concentration, isolated betaxanthins were derivatized according to the "EZ:faast" method prior to quantification of the respective amino compounds released. On a molar basis, betaxanthin contribution to overall amino compound contents was always below 6.4%.

Dynamic simulation of Static Var Compensators in distribution systems

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

Koessler, R.J.

1992-08-01

This paper is a system study guide for the correction of voltage dips due to large motor startups with Static Var Compensators (SVCs). The method utilizes time simulations, which are an important aid in the equipment design and specification. The paper illustrates the process of setting-up a computer model and performing time simulations. The study process is demonstrated through an example, the Shawnee feeder in the Niagara Mohawk Power Corporation service area.

Effect of Medium Supplements on Agrobacterium rhizogenes Mediated Hairy Root Induction from the Callus Tissues of Camellia sinensis var. sinensis

PubMed Central

Rana, Mohammad M.; Han, Zhuo-Xiao; Song, Da-Peng; Liu, Guo-Feng; Li, Da-Xiang; Wan, Xiao-Chun; Karthikeyan, Alagarsamy; Wei, Shu

2016-01-01

Tea (Camellia sinensis L.) is recalcitrant to Agrobacterium-mediated genetic transformation largely due to the bactericidal effects of tea polyphenols and phenolics oxidation induced by necrosis of explant tissue over the process of transformation. In this study, different antioxidants/adsorbents were added as supplements to the co-cultivation and post co-cultivation media to overcome these problems for the transformation improvement. Tea-cotyledon-derived calli were used as explants and Agrobacterium rhizognes strain ATCC 15834 was used as a mediator. Results showed that Agrobacterium growth, virulence (vir) gene expression and browning of explant tissue were greatly influenced by different supplements. Murashige and Skoog (MS) basal salts medium supplemented with 30 g·L−1 sucrose, 0.1 g·L−1 l-glutamine and 5 g·L−1 polyvinylpolypyrrolidone (PVPP) as co-cultivation and post co-cultivation media could maintain these parameters better that ultimately led to significant improvement of hairy root generation efficiency compared to that in the control (MS + 30 g·L−1 sucrose). Additionally, the reporter genes β-glucuronidase (gusA) and cyan fluorescent protein (cfp) were also stably expressed in the transgenic hairy roots. Our study would be helpful in establishing a feasible approach for tea biological studies and genetic improvement of tea varieties. PMID:27428960

Effect of Medium Supplements on Agrobacterium rhizogenes Mediated Hairy Root Induction from the Callus Tissues of Camellia sinensis var. sinensis.

PubMed

Rana, Mohammad M; Han, Zhuo-Xiao; Song, Da-Peng; Liu, Guo-Feng; Li, Da-Xiang; Wan, Xiao-Chun; Karthikeyan, Alagarsamy; Wei, Shu

2016-07-15

Tea (Camellia sinensis L.) is recalcitrant to Agrobacterium-mediated genetic transformation largely due to the bactericidal effects of tea polyphenols and phenolics oxidation induced by necrosis of explant tissue over the process of transformation. In this study, different antioxidants/adsorbents were added as supplements to the co-cultivation and post co-cultivation media to overcome these problems for the transformation improvement. Tea-cotyledon-derived calli were used as explants and Agrobacterium rhizognes strain ATCC 15834 was used as a mediator. Results showed that Agrobacterium growth, virulence (vir) gene expression and browning of explant tissue were greatly influenced by different supplements. Murashige and Skoog (MS) basal salts medium supplemented with 30 g·L(-1) sucrose, 0.1 g·L(-1) l-glutamine and 5 g·L(-1) polyvinylpolypyrrolidone (PVPP) as co-cultivation and post co-cultivation media could maintain these parameters better that ultimately led to significant improvement of hairy root generation efficiency compared to that in the control (MS + 30 g·L(-1) sucrose). Additionally, the reporter genes β-glucuronidase (gusA) and cyan fluorescent protein (cfp) were also stably expressed in the transgenic hairy roots. Our study would be helpful in establishing a feasible approach for tea biological studies and genetic improvement of tea varieties.

Fine root morphological traits determine variation in root respiration of Quercus serrata.

PubMed

Makita, Naoki; Hirano, Yasuhiro; Dannoura, Masako; Kominami, Yuji; Mizoguchi, Takeo; Ishii, Hiroaki; Kanazawa, Yoichi

2009-04-01

Fine root respiration is a significant component of carbon cycling in forest ecosystems. Although fine roots differ functionally from coarse roots, these root types have been distinguished based on arbitrary diameter cut-offs (e.g., 2 or 5 mm). Fine root morphology is directly related to physiological function, but few attempts have been made to understand the relationships between morphology and respiration of fine roots. To examine relationships between respiration rates and morphological traits of fine roots (0.15-1.4 mm in diameter) of mature Quercus serrata Murr., we measured respiration of small fine root segments in the field with a portable closed static chamber system. We found a significant power relationship between mean root diameter and respiration rate. Respiration rates of roots<0.4 mm in mean diameter were high and variable, ranging from 3.8 to 11.3 nmol CO2 g(-1) s(-1), compared with those of larger diameter roots (0.4-1.4 mm), which ranged from 1.8 to 3.0 nmol CO2 g(-1) s(-1). Fine root respiration rate was positively correlated with specific root length (SRL) as well as with root nitrogen (N) concentration. For roots<0.4 mm in diameter, SRL had a wider range (11.3-80.4 m g(-1)) and was more strongly correlated with respiration rate than diameter. Our results indicate that a more detailed classification of fine roots<2.0 mm is needed to represent the heterogeneity of root respiration and to evaluate root biomass and root morphological traits.

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

Baccharis megapotamica var. weirii poisoning in water buffalo (Bubalus bubalis).

PubMed

Oliveira-Filho, José C; Carmo, Priscila M S; Lucena, Ricardo B; Pierezan, Felipe; Barros, Claudio S L

2011-05-01

An outbreak of an acute disease in buffalo (Bubalus bubalis) caused by the ingestion of Baccharis megapotamica var. weirii occurred in the southern region of Brazil. Ten out of 50 buffalo died 24-48 hr after being introduced into a pasture containing abundant amounts of the plant. Factors influencing the ingestion of the plant and consequent toxicosis included hunger, stress caused by shipment, and unfamiliarity with the plant. Clinical signs included serous ocular discharge, incoordination, mild bloat, and muscle trembling. One buffalo was necropsied. Gross findings included dehydration, abundant liquid in the rumen, reddening of the mucosa of forestomachs, abomasum, and intestine, and edema of the wall of the rumen. The main histologic lesions were superficial to full thickness degeneration and necrosis of the stratified epithelium lining the forestomachs, necrosis of the intestinal mucosa, and widespread lymphoid necrosis. A calf (Bos taurus) was fed a single dose of 5 g/kg/body weight of B. megapotamica var. weirii harvested from the same site where the buffalo died. Twenty hours after the administration of the plant this calf died with clinical signs and lesions similar to those observed in the naturally poisoned buffalo. © 2011 The Author(s)

Root gravitropism and root hair development constitute coupled developmental responses regulated by auxin homeostasis in the Arabidopsis root apex.

PubMed

Rigas, Stamatis; Ditengou, Franck Anicet; Ljung, Karin; Daras, Gerasimos; Tietz, Olaf; Palme, Klaus; Hatzopoulos, Polydefkis

2013-03-01

Active polar transport establishes directional auxin flow and the generation of local auxin gradients implicated in plant responses and development. Auxin modulates gravitropism at the root tip and root hair morphogenesis at the differentiation zone. Genetic and biochemical analyses provide evidence for defective basipetal auxin transport in trh1 roots. The trh1, pin2, axr2 and aux1 mutants, and transgenic plants overexpressing PIN1, all showing impaired gravity response and root hair development, revealed ectopic PIN1 localization. The auxin antagonist hypaphorine blocked root hair elongation and caused moderate agravitropic root growth, also leading to PIN1 mislocalization. These results suggest that auxin imbalance leads to proximal and distal developmental defects in Arabidopsis root apex, associated with agravitropic root growth and root hair phenotype, respectively, providing evidence that these two auxin-regulated processes are coupled. Cell-specific subcellular localization of TRH1-YFP in stele and epidermis supports TRH1 engagement in auxin transport, and hence impaired function in trh1 causes dual defects of auxin imbalance. The interplay between intrinsic cues determining root epidermal cell fate through the TTG/GL2 pathway and environmental cues including abiotic stresses modulates root hair morphogenesis. As a consequence of auxin imbalance in Arabidopsis root apex, ectopic PIN1 mislocalization could be a risk aversion mechanism to trigger root developmental responses ensuring root growth plasticity. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

Seedling root targets

Treesearch

Diane L. Haase

2011-01-01

Roots are critical to seedling performance after outplanting. Although root quality is not as quick and simple to measure as shoot quality, target root characteristics should be included in any seedling quality assessment program. This paper provides a brief review of root characteristics most commonly targeted for operational seedling production. These are: root mass...

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

Effect of Root Moisture Content and Diameter on Root Tensile Properties.

PubMed

Yang, Yuanjun; Chen, Lihua; Li, Ning; Zhang, Qiufen

2016-01-01

The stabilization of slopes by vegetation has been a topical issue for many years. Root mechanical characteristics significantly influence soil reinforcement; therefore it is necessary to research into the indicators of root tensile properties. In this study, we explored the influence of root moisture content on tensile resistance and strength with different root diameters and for different tree species. Betula platyphylla, Quercus mongolica, Pinus tabulaeformis, and Larix gmelinii, the most popular tree species used for slope stabilization in the rocky mountainous areas of northern China, were used in this study. A tensile test was conducted after root samples were grouped by diameter and moisture content. The results showedthat:1) root moisture content had a significant influence on tensile properties; 2) slightly loss of root moisture content could enhance tensile strength, but too much loss of water resulted in weaker capacity for root elongation, and consequently reduced tensile strength; 3) root diameter had a strong positive correlation with tensile resistance; and4) the roots of Betula platyphylla had the best tensile properties when both diameter and moisture content being controlled. These findings improve our understanding of root tensile properties with root size and moisture, and could be useful for slope stabilization using vegetation.

Effect of Root Moisture Content and Diameter on Root Tensile Properties

PubMed Central

Yang, Yuanjun; Chen, Lihua; Li, Ning; Zhang, Qiufen

2016-01-01

The stabilization of slopes by vegetation has been a topical issue for many years. Root mechanical characteristics significantly influence soil reinforcement; therefore it is necessary to research into the indicators of root tensile properties. In this study, we explored the influence of root moisture content on tensile resistance and strength with different root diameters and for different tree species. Betula platyphylla, Quercus mongolica, Pinus tabulaeformis, and Larix gmelinii, the most popular tree species used for slope stabilization in the rocky mountainous areas of northern China, were used in this study. A tensile test was conducted after root samples were grouped by diameter and moisture content. The results showedthat:1) root moisture content had a significant influence on tensile properties; 2) slightly loss of root moisture content could enhance tensile strength, but too much loss of water resulted in weaker capacity for root elongation, and consequently reduced tensile strength; 3) root diameter had a strong positive correlation with tensile resistance; and4) the roots of Betula platyphylla had the best tensile properties when both diameter and moisture content being controlled. These findings improve our understanding of root tensile properties with root size and moisture, and could be useful for slope stabilization using vegetation. PMID:27003872

An unusual variant of Trichophyton tonsurans var. sulfureum.

PubMed

Padhye, A A; Weitzman, I; Domenech, E

1994-01-01

A fungus, recovered from a skin lesion of a patient, produced velvety to powdery, white to deep yellow colonies on Sabouraud glucose agar. Microscopically, it produced a large number of cylindric, smooth-walled, three- to eight-celled macroconidia but failed to produce microconidia on a variety of nutritional media such as rice grains, cornmeal dextrose, potato dextrose, Sabouraud glucose, oatmeal and lactrimel agars. It hydrolysed urea in 7 days, perforated hair in vitro and required thiamine for growth. This isolate represents an atypical variant of Trichophyton tonsurans var. sufureum subvar. perforans.

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.

A three-level advanced static VAr compensator

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

Ekanayake, J.B.; Jenkins, N.

1996-01-01

An Advanced Static VAr Compensator (ASVC) employing a three level inverter has been investigated for three phase applications. The paper describes the operating principles of the ASVC using an elementary single phase ASVC circuit. The construction of a hardware model of the three phase, three level ASVC is then presented. The performance of the ASVC is obtained from an experimental study carried out on this laboratory model. The use of the selective harmonic elimination modulation (SHEM) technique to minimize harmonics is explored. Experimental studies have been carried out to determine the speed of response of the scheme by controlling itmore » in a closed loop.« less

Cardenolide glycosides from Elaeodendron australe var. integrifolium.

PubMed

Butler, Mark S; Towerzey, Leanne; Pham, Ngoc B; Hyde, Edward; Wadi, Sao Khemar; Guymer, Gordon P; Quinn, Ronald J

2014-02-01

Extracts from dried leaf and stems of Elaeodendron australe var. integrifolium (Celastraceae) collected in South East Queensland, Australia, were active in an assay that measured Ca(2+) driven expression of IL-2/luciferase designed to identify inhibitors of the ICRAC channel. Bioassay-guided isolation using C18 and polyamide column chromatography, HPLC (Phenyl and C18) and centrifugal partition chromatography (CPC) led to the isolation of digitoxigenin (1) and three cardenolide glycosides, glucoside 2, quinovoside 3 and the new natural product xyloside 4, as the active components with low nM activity in the reporter assay. Copyright © 2013 Elsevier Ltd. All rights reserved.

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)-...

Root distribution and potential interactions between allelopathic rice, sprangletop (Leptochloa spp.), and barnyardgrass (Echinochloa crus-galli) based on ¹³C isotope discrimination analysis.

PubMed

Gealy, David; Moldenhauer, Karen; Duke, Sara

2013-02-01

Weed-suppressive rice cultivars hold promise for improved and more economical weed management in rice. Interactions between roots of rice and weeds are thought to be modulated by the weed-suppressive activity of some rice cultivars, but these phenomena are difficult to measure and not well understood. Thus, above-ground productivity, weed suppression, and root distribution of 11 rice cultivars and two weed species were evaluated in a drill-seeded, flood-irrigated system at Stuttgart, Arkansas, USA in a two-year study. The allelopathic cultivars, PI 312777 and Taichung Native 1 (TN-1), three other weed-suppressive cultivars, three indica-derived breeding selections, and three non-suppressive commercial cultivars were evaluated in field plots infested with barnyardgrass (Echinochloa crus-galli (L.) Beauv.) or bearded sprangletop (sprangletop, Leptochloa fusca (L.) Kunth var. fascicularis (Lam.) N. Snow). The allelopathic cultivars produced more tillers and suppressed both weed species to a greater extent than did the breeding selections or the non-suppressive cultivars. (13)C isotope discrimination analysis of mixed root samples to a depth of 15 cm revealed that the allelopathic cultivars typically produced a greater fraction of their total root mass in the surface 0-5 cm of soil depth compared to the breeding selections or the non-suppressive cultivars, which tended to distribute their roots more evenly throughout the soil profile. These trends in root mass distribution were apparent at both early (pre-flood) and late-season stages in weed-free and weed-infested plots. Cultivar productivity and root distribution generally responded similarly to competition with the two weed species, but barnyardgrass reduced rice yield and root mass more than did sprangletop. These findings demonstrate for the first time that roots of the allelopathic cultivars PI 312777 and TN-1 explore the upper soil profile more thoroughly than do non-suppressive cultivars under weed

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.

A heterogeneous boron distribution in soil influences the poplar root system architecture development

NASA Astrophysics Data System (ADS)

Rees, R.; Robinson, B. H.; Hartmann, S.; Lehmann, E.; Schulin, R.

2009-04-01

Poplars are well suited for the phytomanagement of boron (B)-contaminated sites, due to their high transpiration rate and tolerance to elevated soil B concentrations. However, the uptake and the fate of B in poplar stands are not well understood. This information is crucial to improve the design of phytomanagement systems, where the primary role of poplars is to reduce B leaching by reducing the water flux through the contaminated material. Like other trace elements, B occurs heterogeneously in soils. Concentrations can differ up to an order of magnitude within centimetres. These gradients affect plant root growth and thus via preferential flow along the roots water and mass transport in soils to ground and surface waters. Generally there are three possible reactions of plant roots to patches with elevated trace element concentrations in soils: indifference, avoidance, or foraging. While avoidance or indifference might seem to be the most obvious strategies, foraging cannot be excluded a priori, because of the high demand of poplars for B compared to other tree species. We aimed to determine the rooting strategies of poplars in soils where B is either homo- or heterogeneously distributed. We planted 5 cm cuttings of Populus tremula var. Birmensdorf clones in aluminum (Al) containers with internal dimensions of 64 x 67 x 1.2 cm. The soil used was subsoil from northern Switzerland with a naturally low B and organic C concentration. We setup two treatments and a control with three replicates each. We spiked a bigger and a smaller portion of the soil with the same amount of B(OH)3-salt, in order to obtain soil concentrations of 7.5 mg B kg-1 and 20 mg B kg-1. We filled the containers with (a) un-spiked soil, (b) the 7.5 mg B kg-1 soil and (c) heterogeneously. The heterogeneous treatment consisted of one third 20 mg B kg-1 soil and two thirds control soil. We grew the poplars in a small greenhouse over 2 months and from then on in a climate chamber for another 3 months

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.

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.

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.

Construction of a reference molecular linkage map of globe artichoke (Cynara cardunculus var. scolymus).

PubMed

Portis, E; Mauromicale, G; Mauro, R; Acquadro, A; Scaglione, D; Lanteri, S

2009-12-01

The genome organization of globe artichoke (Cynara cardunculus var. scolymus), unlike other species belonging to Asteraceae (=Compositae) family (i.e. sunflower, lettuce and chicory), remains largely unexplored. The species is highly heterozygous and suffers marked inbreeding depression when forced to self-fertilize. Thus a two-way pseudo-testcross represents the optimal strategy for linkage analysis. Here, we report linkage maps based on the progeny of a cross between globe artichoke (C. cardunculus var. scolymus) and cultivated cardoon (C. cardunculus var. altilis). The population was genotyped using a variety of PCR-based marker platforms, resulting in the identification of 708 testcross markers suitable for map construction. The male map consisted of 177 loci arranged in 17 major linkage groups, spanning 1,015.5 cM, while female map was built with 326 loci arranged into 20 major linkage groups, spanning 1,486.8 cM. The presence of 84 loci shared between these maps and those previously developed from a cross within globe artichoke allowed for map alignment and the definition of 17 homologous linkage groups, corresponding to the haploid number of the species. This will provide a favourable property for QTL scanning; furthermore, as 25 mapped markers (8%) correspond to coding regions, it has an additional value as functional map and might represent an important genetic tool for candidate gene studies in globe artichoke.

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).

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)

Differential Responses of Two Broccoli (Brassica oleracea L. var Italica) Cultivars to Salinity and Nutritional Quality Improvement

PubMed Central

Zaghdoud, Chokri; Alcaraz-López, Carlos; Mota-Cadenas, César; Martínez-Ballesta, María del Carmen; Moreno, Diego A.; Ferchichi, Ali; Carvajal, Micaela

2012-01-01

The comparative responses of two broccoli cultivars (Brassica oleracea var. Italica, cv. Parthenon and cv. Naxos) to a 15 d exposure to different NaCl levels were investigated. Salinity led to increased concentrations of Na+ and Cl− ions in both cultivars, a disruption of the endogenous minerals levels in the shoots and roots—that varied with the cultivar and salt concentration—and decreases in the osmotic potential (Ψπ), root hydraulic conductance (L 0), and stomatal conductance (G s). The reduced biomass of Naxos at moderate NaCl indicates greater sensitivity to salinity, compared with Parthenon. Parthenon accumulated more soluble sugars, for osmotic adjustment, whereas Naxos accumulated proline, which gave the two cultivars differing nutritional characteristics. The total glucosinolates (GSLs) content was not affected by salinity in Parthenon while it decreased significantly in Naxos as a consequence of the decrease in the indole GSL. However, Naxos accumulated more aliphatic GSLs under salt stress than Parthenon, which confers on this cultivar a greater nutritional value when cultivated under salinity.These results suggest that, at distinct salinity levels, each broccoli cultivar adopts a specific strategy, indicating the crucial role of the genetic background on the organoleptic and nutritional properties that each cultivar acquires. PMID:22956893

Comparative kinetics and reciprocal inhibition of nitrate and nitrite uptake in roots of uninduced and induced barley (Hordeum vulgare L.) seedlings

NASA Technical Reports Server (NTRS)

Aslam, M.; Travis, R. L.; Huffaker, R. C.

1992-01-01

Nitrate and NO2- transport by roots of 8-day-old uninduced and induced intact barley (Hordeum vulgare L. var CM 72) seedlings were compared to kinetic patterns, reciprocal inhibition of the transport systems, and the effect of the inhibitor, p-hydroxymercuribenzoate. Net uptake of NO3- and NO2- was measured by following the depletion of the ions from the uptake solutions. The roots of uninduced seedlings possessed a low concentration, saturable, low Km, possibly a constitutive uptake system, and a linear system for both NO3- and NO2-. The low Km system followed Michaelis-Menten kinetics and approached saturation between 40 and 100 micromolar, whereas the linear system was detected between 100 and 500 micromolar. In roots of induced seedlings, rates for both NO3- and NO2- uptake followed Michaelis-Menten kinetics and approached saturation at about 200 micromolar. In induced roots, two kinetically identifiable transport systems were resolved for each anion. At the lower substrate concentrations, less than 10 micromolar, the apparent low Kms of NO3- and NO2- uptake were 7 and 9 micromolar, respectively, and were similar to those of the low Km system in uninduced roots. At substrate concentrations between 10 and 200 micromolar, the apparent high Km values of NO3- uptake ranged from 34 to 36 micromolar and of NO2- uptake ranged from 41 to 49 micromolar. A linear system was also found in induced seedlings at concentrations above 500 micromolar. Double reciprocal plots indicated that NO3- and NO2- inhibited the uptake of each other competitively in both uninduced and induced seedlings; however, Ki values showed that NO3- was a more effective inhibitor than NO2-. Nitrate and NO2- transport by both the low and high Km systems were greatly inhibited by p-hydroxymercuribenzoate, whereas the linear system was only slightly inhibited.

Root Tip Shape Governs Root Elongation Rate under Increased Soil Strength1[OPEN

PubMed Central

Kirchgessner, Norbert; Walter, Achim

2017-01-01

Increased soil strength due to soil compaction or soil drying is a major limitation to root growth and crop productivity. Roots need to exert higher penetration force, resulting in increased penetration stress when elongating in soils of greater strength. This study aimed to quantify how the genotypic diversity of root tip geometry and root diameter influences root elongation under different levels of soil strength and to determine the extent to which roots adjust to increased soil strength. Fourteen wheat (Triticum aestivum) varieties were grown in soil columns packed to three bulk densities representing low, moderate, and high soil strength. Under moderate and high soil strength, smaller root tip radius-to-length ratio was correlated with higher genotypic root elongation rate, whereas root diameter was not related to genotypic root elongation. Based on cavity expansion theory, it was found that smaller root tip radius-to-length ratio reduced penetration stress, thus enabling higher root elongation rates in soils with greater strength. Furthermore, it was observed that roots could only partially adjust to increased soil strength. Root thickening was bounded by a maximum diameter, and root tips did not become more acute in response to increased soil strength. The obtained results demonstrated that root tip geometry is a pivotal trait governing root penetration stress and root elongation rate in soils of greater strength. Hence, root tip shape needs to be taken into account when selecting for crop varieties that may tolerate high soil strength. PMID:28600344

Correlation of root dentin thickness and length of roots in mesial roots of mandibular molars.

PubMed

Dwivedi, Shweta; Dwivedi, Chandra Dhar; Mittal, Neelam

2014-09-01

The purpose of this study was to analyze the relation of tooth length and distal wall thickness of mesial roots in mandibular molars at different locations (ie, 2 mm below the furcation and at the junction between the middle and apical third). Forty-five mandibular first molars were taken, and the length of each tooth was measured. Then, specimens were divided into three groups according to their length: group I-long (24.2 mm ± 1.8), group II-medium (21 mm ± 1.5) and group III-short (16.8 mm ± 1.8). mesial root of each marked at two levels - at 2 mm below the furcation as well as at junction of apical and middle third of roots. The minimum thickness of the distal root dentine associated with the buccal and lingual canals of the mesial roots was measured, The distance between the buccal and lingual canals and the depth of concavity in the distal surface of the mesial roots were also measured. Statistical analysis was performed by using analysis of variance and the Student-Newman-Keuls test. The minimum thickness of the distal wall of the mesiobuccal canal was significantly different (P < .001) between groups 1 (long) and 3 (short). Distal wall thickness of the mesiobuccal root and distal concavity of the mesial root of mandibular first molars were found to be thinner in longer teeth compared with shorter teeth. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

VAR2CSA signatures of high Plasmodium falciparum parasitemia in the placenta.

PubMed

Rovira-Vallbona, Eduard; Monteiro, Isadora; Bardají, Azucena; Serra-Casas, Elisa; Neafsey, Daniel E; Quelhas, Diana; Valim, Clarissa; Alonso, Pedro; Dobaño, Carlota; Ordi, Jaume; Menéndez, Clara; Mayor, Alfredo

2013-01-01

Plasmodium falciparum infected erythrocytes (IE) accumulate in the placenta through the interaction between Duffy-binding like (DBL) domains of parasite-encoded ligand VAR2CSA and chondroitin sulphate-A (CSA) receptor. Polymorphisms in these domains, including DBL2X and DBL3X, may affect their antigenicity or CSA-binding affinity, eventually increasing parasitemia and its adverse effects on pregnancy outcomes. A total of 373 DBL2X and 328 DBL3X sequences were obtained from transcripts of 20 placental isolates infecting Mozambican women, resulting in 176 DBL2X and 191 DBL3X unique sequences at the protein level. Sequence alignments were divided in segments containing combinations of correlated polymorphisms and the association of segment sequences with placental parasite density was tested using Bonferroni corrected regression models, taking into consideration the weight of each sequence in the infection. Three DBL2X and three DBL3X segments contained signatures of high parasite density (P<0.003) that were highly prevalent in the parasite population (49-91%). Identified regions included a flexible loop that contributes to DBL3X-CSA interaction and two DBL3X motifs with evidence of positive natural selection. Limited antibody responses against signatures of high parasite density among malaria-exposed pregnant women could not explain the increased placental parasitemia. These results suggest that a higher binding efficiency to CSA rather than reduced antigenicity might provide a biological advantage to parasites with high parasite density signatures in VAR2CSA. Sequences contributing to high parasitemia may be critical for the functional characterization of VAR2CSA and the development of tools against placental malaria.

Root diversity in alpine plants: root length, tensile strength and plant age

NASA Astrophysics Data System (ADS)

Pohl, M.; Stroude, R.; Körner, C.; Buttler, A.; Rixen, C.

2009-04-01

A high diversity of plant species and functional groups is hypothesised to increase the diversity of root types and their subsequent effects for soil stability. However, even basic data on root characteristics of alpine plants are very scarce. Therefore, we determined important root characteristics of 13 plant species from different functional groups, i.e. grasses, herbs and shrubs. We excavated the whole root systems of 62 plants from a machine-graded ski slope at 2625 m a.s.l. and analysed the rooting depth, the horizontal root extension, root length and diameter. Single roots of plant species were tested for tensile strength. The age of herbs and shrubs was determined by growth-ring analysis. Root characteristics varied considerably between both plant species and functional groups. The rooting depth of different species ranged from 7.2 ± 0.97 cm to 20.5 ± 2.33 cm, but was significantly larger in the herb Geum reptans (70.8 ± 10.75 cm). The woody species Salix breviserrata reached the highest horizontal root extensions (96.8 ± 25.5 cm). Most plants had their longest roots in fine diameter classes (0.5

Meniscus root repair.

PubMed

Vyas, Dharmesh; Harner, Christopher D

2012-06-01

Root tears are a subset of meniscal injuries that result in significant knee joint pathology. Occurring on either the medial or lateral side, root tears are defined as radial tears or avulsions of the posterior horn attachment to bone. After a root tear, there is a significant increase in tibio-femoral contact pressure concomitant with altered knee joint kinematics. Previous cadaver studies from our institution have shown that root repair of the medial meniscus is successful in restoring joint biomechanics to within normal limits. Indications for operative management of meniscal root tears include (1) a symptomatic medial meniscus root tear with minimal arthritis and having failed non-operative treatment, and (2) a lateral root tear in associated with an ACL tear. In this review, we describe diagnosis, imaging, patient selection, and arthroscopic surgical technique of medial and lateral meniscus root injuries. In addition we highlight the pearls of repair technique, associated complications, post-operative rehabilitation regimen, and expected outcomes.

Root anatomical phenes predict root penetration ability and biomechanical properties in maize (Zea Mays)

PubMed Central

Chimungu, Joseph G.; Loades, Kenneth W.; Lynch, Jonathan P.

2015-01-01

The ability of roots to penetrate hard soil is important for crop productivity but specific root phenes contributing to this ability are poorly understood. Root penetrability and biomechanical properties are likely to vary in the root system dependent on anatomical structure. No information is available to date on the influence of root anatomical phenes on root penetrability and biomechanics. Root penetration ability was evaluated using a wax layer system. Root tensile and bending strength were evaluated in plant roots grown in the greenhouse and in the field. Root anatomical phenes were found to be better predictors of root penetrability than root diameter per se and associated with smaller distal cortical region cell size. Smaller outer cortical region cells play an important role in stabilizing the root against ovalization and reducing the risk of local buckling and collapse during penetration, thereby increasing root penetration of hard layers. The use of stele diameter was found to be a better predictor of root tensile strength than root diameter. Cortical thickness, cortical cell count, cortical cell wall area and distal cortical cell size were stronger predictors of root bend strength than root diameter. Our results indicate that root anatomical phenes are important predictors for root penetrability of high-strength layers and root biomechanical properties. PMID:25903914

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.

Light as stress factor to plant roots – case of root halotropism

PubMed Central

Yokawa, Ken; Fasano, Rossella; Kagenishi, Tomoko; Baluška, František

2014-01-01

Despite growing underground, largely in darkness, roots emerge to be very sensitive to light. Recently, several important papers have been published which reveal that plant roots not only express all known light receptors but also that their growth, physiology and adaptive stress responses are light-sensitive. In Arabidopsis, illumination of roots speeds-up root growth via reactive oxygen species-mediated and F-actin dependent process. On the other hand, keeping Arabidopsis roots in darkness alters F-actin distribution, polar localization of PIN proteins as well as polar transport of auxin. Several signaling components activated by phytohormones are overlapping with light-related signaling cascade. We demonstrated that the sensitivity of roots to salinity is altered in the light-grown Arabidopsis roots. Particularly, light-exposed roots are less effective in their salt-avoidance behavior known as root halotropism. Here we discuss these new aspects of light-mediated root behavior from cellular, physiological and evolutionary perspectives. PMID:25566292

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

Psoralen production in hairy roots and adventitious roots cultures of Psoralea coryfolia.

PubMed

Baskaran, P; Jayabalan, N

2009-07-01

Psoralea corylifolia is an endangered plant producing various compounds of medical importance. Adventitious roots and hairy roots were induced in cultures prepared from hypocotyl explants. Psoralen content was evaluated in both root types grown either in suspension cultures or on agar solidified medium. Psoralen content was approximately 3 mg g(-1) DW in suspension grown hairy roots being higher than in solid grown hairy roots and in solid and suspension-grown adventitious roots.

Comparing root architectural models

NASA Astrophysics Data System (ADS)

Schnepf, Andrea; Javaux, Mathieu; Vanderborght, Jan

2017-04-01

Plant roots play an important role in several soil processes (Gregory 2006). Root architecture development determines the sites in soil where roots provide input of carbon and energy and take up water and solutes. However, root architecture is difficult to determine experimentally when grown in opaque soil. Thus, root architectural models have been widely used and been further developed into functional-structural models that are able to simulate the fate of water and solutes in the soil-root system (Dunbabin et al. 2013). Still, a systematic comparison of the different root architectural models is missing. In this work, we focus on discrete root architecture models where roots are described by connected line segments. These models differ (a) in their model concepts, such as the description of distance between branches based on a prescribed distance (inter-nodal distance) or based on a prescribed time interval. Furthermore, these models differ (b) in the implementation of the same concept, such as the time step size, the spatial discretization along the root axes or the way stochasticity of parameters such as root growth direction, growth rate, branch spacing, branching angles are treated. Based on the example of two such different root models, the root growth module of R-SWMS and RootBox, we show the impact of these differences on simulated root architecture and aggregated information computed from this detailed simulation results, taking into account the stochastic nature of those models. References Dunbabin, V.M., Postma, J.A., Schnepf, A., Pagès, L., Javaux, M., Wu, L., Leitner, D., Chen, Y.L., Rengel, Z., Diggle, A.J. Modelling root-soil interactions using three-dimensional models of root growth, architecture and function (2013) Plant and Soil, 372 (1-2), pp. 93 - 124. Gregory (2006) Roots, rhizosphere and soil: the route to a better understanding of soil science? European Journal of Soil Science 57: 2-12.

Spatial Distribution of Root and Crown Rot Fungi Associated With Winter Wheat in the North China Plain and Its Relationship With Climate Variables

PubMed Central

Xu, Fei; Yang, Gongqiang; Wang, Junmei; Song, Yuli; Liu, Lulu; Zhao, Kai; Li, Yahong; Han, Zihang

2018-01-01

The distribution frequency of pathogenic fungi associated with root and crown rot of winter wheat (Triticum aestivum) from 104 fields in the North China Plain was determined during the period from 2013 to 2016. The four most important species identified were Bipolaris sorokiniana (24.0% from roots; 33.7% from stems), Fusarium pseudograminearum (14.9% from roots; 27.8% from stems), Rhizoctonia cerealis (1.7% from roots; 4.4% from stems), and Gaeumannomyces graminis var. tritici (9.8% from roots; 4.4% from stems). We observed that the recovered species varied with the agronomic zone. Fusarium pseudograminearum was predominant in regions 1 and 3, whereas F. graminearum, F. acuminatum, and R. cerealis were predominant in regions 2 and 4. The incidence of F. pseudograminearum and R. cerealis was significantly different between regions 1 and 4, while no significant association was found in the distribution of the other species and the agronomic zones. A negative correlation between the frequency of occurrence of F. pseudograminearum and mean annual precipitation during 2013–2016 (r = −0.71; P < 0.01) in the North China Plain and a positive correlation between the mean annual precipitation during 2013–2016 and the frequency of occurrence of F. asiaticum (r = 0.74; P < 0.01) were observed. Several Fusarium species were also found with low frequencies of ~2.1%−3.4 % (F. graminearum, F. acuminatum, and F. sinensis) and ~0.1%−1.3% (F. equiseti, F. oxysporum, F. proliferatum, F. culmorum, F. avenaceum, and F. asiaticum). In more than 93% of the fields, from the root and crown tissues of wheat, two or more root and crown rot species were isolated. The coexistence of Fusarium spp. and B. sorokiniana in one field (65.4%) or in individual plants (11.6%) was more common than for the other species combinations. Moreover, this is the first report on the association between F. sinensis and root and crown rot of wheat. Our results would be useful in the framing guidelines for

Root hairs aid soil penetration by anchoring the root surface to pore walls

PubMed Central

Bengough, A. Glyn; Loades, Kenneth; McKenzie, Blair M.

2016-01-01

The physical role of root hairs in anchoring the root tip during soil penetration was examined. Experiments using a hairless maize mutant (Zea mays: rth3–3) and its wild-type counterpart measured the anchorage force between the primary root of maize and the soil to determine whether root hairs enabled seedling roots in artificial biopores to penetrate sandy loam soil (dry bulk density 1.0–1.5g cm−3). Time-lapse imaging was used to analyse root and seedling displacements in soil adjacent to a transparent Perspex interface. Peak anchorage forces were up to five times greater (2.5N cf. 0.5N) for wild-type roots than for hairless mutants in 1.2g cm−3 soil. Root hair anchorage enabled better soil penetration for 1.0 or 1.2g cm−3 soil, but there was no significant advantage of root hairs in the densest soil (1.5g cm−3). The anchorage force was insufficient to allow root penetration of the denser soil, probably because of less root hair penetration into pore walls and, consequently, poorer adhesion between the root hairs and the pore walls. Hairless seedlings took 33h to anchor themselves compared with 16h for wild-type roots in 1.2g cm−3 soil. Caryopses were often pushed several millimetres out of the soil before the roots became anchored and hairless roots often never became anchored securely.The physical role of root hairs in anchoring the root tip may be important in loose seed beds above more compact soil layers and may also assist root tips to emerge from biopores and penetrate the bulk soil. PMID:26798027

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

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...

Root canal irrigants

PubMed Central

Kandaswamy, Deivanayagam; Venkateshbabu, Nagendrababu

2010-01-01

Successful root canal therapy relies on the combination of proper instrumentation, irrigation, and obturation of the root canal. Of these three essential steps of root canal therapy, irrigation of the root canal is the most important determinant in the healing of the periapical tissues. The primary endodontic treatment goal must thus be to optimize root canal disinfection and to prevent reinfection. In this review of the literature, various irrigants and the interactions between irrigants are discussed. We performed a Medline search for English-language papers published untill July 2010. The keywords used were ‘root canal irrigants’ and ‘endodontic irrigants.’ The reference lists of each article were manually checked for additional articles of relevance. PMID:21217955

Foraging strategies in trees of different root morphology: the role of root lifespan.

PubMed

Adams, Thomas S; McCormack, M Luke; Eissenstat, David M

2013-09-01

Resource exploitation of patches is influenced not simply by the rate of root production in the patches but also by the lifespan of the roots inhabiting the patches. We examined the effect of sustained localized nitrogen (N) fertilization on root lifespan in four tree species that varied widely in root morphology and presumed foraging strategy. The study was conducted in a 12-year-old common garden in central Pennsylvania using a combination of data from minirhizotron and root in-growth cores. The two fine-root tree species, Acer negundo L. and Populus tremuloides Michx., exhibited significant increases in root lifespan with local N fertilization; no significant responses were observed in the two coarse-root tree species, Sassafras albidum Nutt. and Liriodendron tulipifera L. Across species, coarse-root tree species had longer median root lifespan than fine-root tree species. Localized N fertilization did not significantly increase the N concentration or the respiration of the roots growing in the N-rich patch. Our results suggest that some plant species appear to regulate the lifespan of different portions of their root system to improve resource acquisition while other species do not. Our results are discussed in the context of different strategies of foraging of nutrient patches in species of different root morphology.

X-ray computed tomography uncovers root-root interactions: quantifying spatial relationships between interacting root systems in three dimensions.

PubMed

Paya, Alexander M; Silverberg, Jesse L; Padgett, Jennifer; Bauerle, Taryn L

2015-01-01

Research in the field of plant biology has recently demonstrated that inter- and intra-specific interactions belowground can dramatically alter root growth. Our aim was to answer questions related to the effect of inter- vs. intra-specific interactions on the growth and utilization of undisturbed space by fine roots within three dimensions (3D) using micro X-ray computed tomography. To achieve this, Populus tremuloides (quaking aspen) and Picea mariana (black spruce) seedlings were planted into containers as either solitary individuals, or inter-/intra-specific pairs, allowed to grow for 2 months, and 3D metrics developed in order to quantify their use of belowground space. In both aspen and spruce, inter-specific root interactions produced a shift in the vertical distribution of the root system volume, and deepened the average position of root tips when compared to intra-specifically growing seedlings. Inter-specific interactions also increased the minimum distance between root tips belonging to the same root system. There was no effect of belowground interactions on the radial distribution of roots, or the directionality of lateral root growth for either species. In conclusion, we found that significant differences were observed more often when comparing controls (solitary individuals) and paired seedlings (inter- or intra-specific), than when comparing inter- and intra-specifically growing seedlings. This would indicate that competition between neighboring seedlings was more responsible for shifting fine root growth in both species than was neighbor identity. However, significant inter- vs. intra-specific differences were observed, which further emphasizes the importance of biological interactions in competition studies.

Geranylated 2-arylbenzofurans from Morus alba var. tatarica and their α-glucosidase and protein tyrosine phosphatase 1B inhibitory activities.

PubMed

Zhang, Ya-Long; Luo, Jian-Guang; Wan, Chuan-Xing; Zhou, Zhong-Bo; Kong, Ling-Yi

2014-01-01

Ten new geranylated 2-arylbenzofuran derivatives, including two monoterpenoid 2-arylbenzofurans (1 and 2), two geranylated 2-arylbenzofuran enantiomers (3a and 3b), and six geranylated 2-arylbenzofurans (4-9), along with four known 2-arylbenzofurans (10-13) were isolated from the root bark of Morus alba var. tatarica. Their structures and relative configurations were established on the basis of spectroscopic data analysis. Compounds 3-7 with one asymmetric carbon at C-7″ were supposed to be enantiomeric mixtures confirmed by chiral HPLC analysis, and the absolute configurations of each enantiomer in 3-7 were determined by Rh2(OCOCF3)4-induced CD and Snatzke's method. The enantiomers with the substituting group at C-2' exhibited better resolutions on a Chiralpak AD-H column than those with the substituting group at C-4'. Compounds 1-7, 10, 11 and 13, showed α-glucosidase inhibitory activities with IC50 values of 11.9-131.9 μM, and compounds 1 and 9-13 inhibited protein tyrosine phosphatase 1B (PTP1B) with IC50 values of 7.9-38.1 μM. Copyright © 2013 Elsevier B.V. All rights reserved.

Root hairs aid soil penetration by anchoring the root surface to pore walls.

PubMed

Bengough, A Glyn; Loades, Kenneth; McKenzie, Blair M

2016-02-01

The physical role of root hairs in anchoring the root tip during soil penetration was examined. Experiments using a hairless maize mutant (Zea mays: rth3-3) and its wild-type counterpart measured the anchorage force between the primary root of maize and the soil to determine whether root hairs enabled seedling roots in artificial biopores to penetrate sandy loam soil (dry bulk density 1.0-1.5g cm(-3)). Time-lapse imaging was used to analyse root and seedling displacements in soil adjacent to a transparent Perspex interface. Peak anchorage forces were up to five times greater (2.5N cf. 0.5N) for wild-type roots than for hairless mutants in 1.2g cm(-3) soil. Root hair anchorage enabled better soil penetration for 1.0 or 1.2g cm(-3) soil, but there was no significant advantage of root hairs in the densest soil (1.5g cm(-3)). The anchorage force was insufficient to allow root penetration of the denser soil, probably because of less root hair penetration into pore walls and, consequently, poorer adhesion between the root hairs and the pore walls. Hairless seedlings took 33h to anchor themselves compared with 16h for wild-type roots in 1.2g cm(-3) soil. Caryopses were often pushed several millimetres out of the soil before the roots became anchored and hairless roots often never became anchored securely.The physical role of root hairs in anchoring the root tip may be important in loose seed beds above more compact soil layers and may also assist root tips to emerge from biopores and penetrate the bulk soil. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Measurements of water uptake of maize roots: the key function of lateral roots

NASA Astrophysics Data System (ADS)

Ahmed, M. A.; Zarebanadkouki, M.; Kroener, E.; Kaestner, A.; Carminati, A.

2014-12-01

Maize (Zea mays L.) is one of the most important crop worldwide. Despite its importance, there is limited information on the function of different root segments and root types of maize in extracting water from soils. Therefore, the aim of this study was to investigate locations of root water uptake in maize. We used neutron radiography to: 1) image the spatial distribution of maize roots in soil and 2) trace the transport of injected deuterated water (D2O) in soil and roots. Maizes were grown in aluminum containers (40×38×1 cm) filled with a sandy soil. When the plants were 16 days old, we injected D2O into selected soil regions containing primary, seminal and lateral roots. The experiments were performed during the day (transpiring plants) and night (not transpiring plants). The transport of D2O into roots was simulated using a new convection-diffusion numerical model of D2O transport into roots. By fitting the observed D2O transport we quantified the diffusional permeability and the water uptake of the different root segments. The maize root architecture consisted of a primary root, 4-5 seminal roots and many lateral roots connected to the primary and seminal roots. Laterals emerged from the proximal 15 cm of the primary and seminal roots. Water uptake occurred primarily in lateral roots. Lateral roots had the highest diffusional permeability (9.4×10-7), which was around six times higher that the diffusional permeability of the old seminal segments (1.4×10-7), and two times higher than the diffusional permeability of the young seminal segments (4.7×10-7). The radial flow of D2O into the lateral (6.7×10-5 ) was much higher than in the young seminal roots (1.1×10-12). The radial flow of D2O into the old seminal was negligible. We concluded that the function of the primary and seminal roots was to collect water from the lateral roots and transport it to the shoot. A maize root system with lateral roots branching from deep primary and seminal roots would be

Depth and Diameter of the Parent Roots of Aspen Root Suckers

Treesearch

Robert E. Farmer

1962-01-01

Studies of the Populus tremuloides root system by Day (1944), Sandberg (1951) and Barnes (1959) have all shown lateral roots extending as much as 30 feet from tree base. These roots may branch extensively and sometimes exhibit an "undulating" growth habit. According to the above authors, suckers occur on the segments of these lateral roots...

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

Sorghum root-system classification in contrasting P environments reveals three main rooting types and root-architecture-related marker-trait associations.

PubMed

Parra-Londono, Sebastian; Kavka, Mareike; Samans, Birgit; Snowdon, Rod; Wieckhorst, Silke; Uptmoor, Ralf

2018-02-12

Roots facilitate acquisition of macro- and micronutrients, which are crucial for plant productivity and anchorage in the soil. Phosphorus (P) is rapidly immobilized in the soil and hardly available for plants. Adaptation to P scarcity relies on changes in root morphology towards rooting systems well suited for topsoil foraging. Root-system architecture (RSA) defines the spatial organization of the network comprising primary, lateral and stem-derived roots and is important for adaptation to stress conditions. RSA phenotyping is a challenging task and essential for understanding root development. In this study, 19 traits describing RSA were analysed in a diversity panel comprising 194 sorghum genotypes, fingerprinted with a 90-k single-nucleotide polymorphism (SNP) array and grown under low and high P availability. Multivariate analysis was conducted and revealed three different RSA types: (1) a small root system; (2) a compact and bushy rooting type; and (3) an exploratory root system, which might benefit plant growth and development if water, nitrogen (N) or P availability is limited. While several genotypes displayed similar rooting types in different environments, others responded to P scarcity positively by developing more exploratory root systems, or negatively with root growth suppression. Genome-wide association studies revealed significant quantitative trait loci (P < 2.9 × 10-6) on chromosomes SBI-02, SBI-03, SBI-05 and SBI-09. Co-localization of significant and suggestive (P < 5.7 × 10-5) associations for several traits indicated hotspots controlling root-system development on chromosomes SBI-02 and SBI-03. Sorghum genotypes with a compact, bushy and shallow root system provide potential adaptation to P scarcity in the field by allowing thorough topsoil foraging, while genotypes with an exploratory root system may be advantageous if N or water is the limiting factor, although such genotypes showed highest P uptake levels under the artificial conditions

RootGraph: a graphic optimization tool for automated image analysis of plant roots

PubMed Central

Cai, Jinhai; Zeng, Zhanghui; Connor, Jason N.; Huang, Chun Yuan; Melino, Vanessa; Kumar, Pankaj; Miklavcic, Stanley J.

2015-01-01

This paper outlines a numerical scheme for accurate, detailed, and high-throughput image analysis of plant roots. In contrast to existing root image analysis tools that focus on root system-average traits, a novel, fully automated and robust approach for the detailed characterization of root traits, based on a graph optimization process is presented. The scheme, firstly, distinguishes primary roots from lateral roots and, secondly, quantifies a broad spectrum of root traits for each identified primary and lateral root. Thirdly, it associates lateral roots and their properties with the specific primary root from which the laterals emerge. The performance of this approach was evaluated through comparisons with other automated and semi-automated software solutions as well as against results based on manual measurements. The comparisons and subsequent application of the algorithm to an array of experimental data demonstrate that this method outperforms existing methods in terms of accuracy, robustness, and the ability to process root images under high-throughput conditions. PMID:26224880

GLO-Roots: An imaging platform enabling multidimensional characterization of soil-grown root systems

DOE PAGES

Rellan-Alvarez, Ruben; Lobet, Guillaume; Lindner, Heike; ...

2015-08-19

Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction, and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated-imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that uses luminescence-based reporters to enable studies of root architecture and gene expression patterns in soil-grown, light-shielded roots. We have developed image analysis algorithms that allow themore » spatial integration of soil properties, gene expression, and root system architecture traits. We propose GLO-Roots as a system that has great utility in presenting environmental stimuli to roots in ways that evoke natural adaptive responses and in providing tools for studying the multi-dimensional nature of such processes.« less

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

Global transcriptome analysis profiles metabolic pathways in traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao

PubMed Central

2015-01-01

Background Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao (A. mongolicus, family Leguminosae) is one of the most important traditional Chinese herbs. Among many secondary metabolites it produces, the effective bioactive constituents include isoflavonoids and triterpene saponins. The genomic resources regarding the biosynthesis of these metabolites in A. mongolicus are limited. Although roots are the primary material harvested for medical use, the biosynthesis of the bioactive compounds and its regulation in A. mongolicus are not well understood. Therefore, a global transcriptome analysis on A. mongolicus tissues was performed to identify the genes essential for the metabolism and to profile their expression patterns in greater details. Results RNA-sequencing was performed for three different A. mongolicus tissues: leaf, stem, and root, using the Illumina Hiseq2000 platform. A total of 159.5 million raw sequence reads were generated, and assembled into 186,324 unigenes with an N50 of 1,524bp. Among them, 129,966 unigenes (~69.7%) were annotated using four public databases (Swiss-Prot, TrEMBL, CDD, Pfam), and 90,202, 63,946, and 78,326 unigenes were found to express in leaves, roots, and stems, respectively. A total of 8,025 transcription factors (TFs) were identified, in which the four largest families, bHLH, MYB, C3H, and WRKY, were implicated in regulation of tissue development, metabolisms, stress response, etc. Unigenes associated with secondary metabolism, especially those with isolavonoids and triterpene saponins biosynthesis were characterized and profiled. Most genes involved in the isoflavonoids biosynthesis had the lowest expression in the leaves, and the highest in the stems. For triterpene saponin biosynthesis, we found the genes in MVA and non-MVA pathways were differentially expressed among three examined tissues, indicating the parallel but compartmentally separated biosynthesis pathways of IPP and DMAPP in A. mongolicus. The first

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...

Physicochemical traits of Dekoko (Pisum sativum var. abyssinicum) seeds.

PubMed

Yemane, Asgedom; Skjelvåg, Arne O

2003-01-01

Dekoko (Pisum sativum var. abyssinicum) has high appreciation for its taste and obtains a premium price in local markets compared to Ater (Pisum sativum var. sativum). However, data on the physicochemical traits of Dekoko seeds were lacking. This paper reports on the physicochemical features of Dekoko and compares the results with that of Ater. Seed weight and seed volume were 36 and 30%, respectively, higher in Ater, while water absorption, percent seed swelling, and percent husk were higher in Dekoko. Cooking time was shorter for Dekoko than Ater seeds. Decortication reduced cooking time on average by 39 and 45 min in Dekoko and Ater, respectively. Cotyledon flour of Dekoko contained 251 g crude protein, 19 g fat, 31.7 g total sugars, 370 g starch, and 130 g neutral detergent fiber per kilogram DM. These traits were significantly higher in Dekoko than in Ater, except for starch, which was higher in the latter. Arginine, asparagine, and glutamine occurred in larger proportions, and collectively contributed about 39% to the total amino acids in both varieties. Lysine contributed about 7%, while sulfur containing amino acids constituted about 3.0 and 2.3% of the total amino acids in Dekoko and Ater, respectively. Ca and Mg were higher in Ater, while P was higher in Dekoko. Based on the observations it was concluded that Dekoko is a suitable supplementary protein source for a cereal-based diet.

Access to mycorrhizal networks and roots of trees: importance for seedling survival and resource transfer.

PubMed

Teste, François P; Simard, Suzanne W; Durall, Daniel M; Guy, Robert D; Jones, Melanie D; Schoonmaker, Amanda L

2009-10-01

Mycorrhizal networks (MNs) are fungal hyphae that connect roots of at least two plants. It has been suggested that these networks are ecologically relevant because they may facilitate interplant resource transfer and improve regeneration dynamics. This study investigated the effects of MNs on seedling survival, growth and physiological responses, interplant resource (carbon and nitrogen) transfer, and ectomycorrhizal (EM) fungal colonization of seedlings by trees in dry interior Douglas-fir (Pseudotsuga menziesii var. glauca) forests. On a large, recently harvested site that retained some older trees, we established 160 isolated plots containing pairs of older Douglas-fir "donor" trees and either manually sown seed or planted Douglas-fir "receiver" seedlings. Seed- and greenhouse-grown seedlings were sown and planted into four mesh treatments that served to restrict MN access (i.e., planted into mesh bags with 0.5-, 35-, 250-microm pores, or without mesh). Older trees were pulse labeled with carbon (13CO2) and nitrogen (15NH4(15)NO3) to quantify resource transfer. After two years, seedlings grown from seed in the field had the greatest survival and received the greatest amounts of transferred carbon (0.0063% of donor photo-assimilates) and nitrogen (0.0018%) where they were grown without mesh; however, planted seedlings were not affected by access to tree roots and hyphae. Size of "donor" trees was inversely related to the amount of carbon transferred to seedlings. The potential for MNs to form was high (based on high similarity of EM communities between hosts), and MN-mediated colonization appeared only to be important for seedlings grown from seed in the field. These results demonstrate that MNs and mycorrhizal roots of trees may be ecologically important for natural regeneration in dry forests, but it is still uncertain whether resource transfer is an important mechanism underlying seedling establishment.

Growth overcompensation against O3 exposure in two Japanese oak species, Quercus mongolica var. crispula and Quercus serrata, grown under elevated CO2.

PubMed

Kitao, Mitsutoshi; Komatsu, Masabumi; Yazaki, Kenichi; Kitaoka, Satoshi; Tobita, Hiroyuki

2015-11-01

To assess the effects of elevated concentrations of carbon dioxide (CO2) and ozone (O3) on the growth of two mid-successional oak species native to East Asia, Quercus mongolica var. crispula and Quercus serrata, we measured gas exchange and biomass allocation in seedlings (initially 1-year-old) grown under combinations of elevated CO2 (550 μmol mol(-1)) and O3 (twice-ambient) for two growing seasons in an open-field experiment in which root growth was not limited. Both the oak species showed a significant growth enhancement under the combination of elevated CO2 and O3 (indicated by total dry mass; over twice of ambient-grown plants, p < .05), which probably resulted from a preferable biomass partitioning into leaves induced by O3 and a predominant enhancement of photosynthesis under elevated CO2. Such an over-compensative response in the two Japanese oak species resulted in greater plant growth under the combination of elevated CO2 and O3 than elevated CO2 alone. Copyright © 2015 Elsevier Ltd. All rights reserved.

Specialized 'dauciform' roots of Cyperaceae are structurally distinct, but functionally analogous with 'cluster' roots.

PubMed

Shane, Michael W; Cawthray, Gregory R; Cramer, Michael D; Kuo, John; Lambers, Hans

2006-10-01

When grown in nutrient solutions of extremely low [P] (roots, which are short and carrot shaped, and produce dense numbers of long root hairs. It has been suggested that dauciform roots of monocotyledonous sedges function to acquire P from nutrient-poor, P-fixing soils in a manner similar to that of cluster (proteoid) roots developed by some dicotyledonous species, but without evidence to substantiate this claim. To elucidate the ecophysiological role of dauciform roots, we assessed carboxylate exudation, internal carboxylate and P concentrations and O(2) uptake rates during dauciform root development. We showed that O(2) consumption was fastest [9 nmol O(2) g(-1) fresh mass (FM) s(-1)] and root [P] greatest (0.4 mg P g(-1) FM) when dauciform roots were young and rapidly developing. Citrate was the most abundant carboxylate in root tissues at all developmental stages, and was most concentrated (22.2 micromol citrate g(-1) FM) in young dauciform roots, decreasing by more than half in mature dauciform roots. Peak citrate-exudation rates (1.7 nmol citrate g(-1) FM s(-1)) occurred from mature dauciform roots, and were approximately an order of magnitude faster than those from roots of species without root clusters, and similar to those of mature proteoid (cluster) roots of Proteaceae. Both developing and mature dauciform roots had the capacity to acidify (but not alkalinize) the rhizosphere. Anatomical studies showed that epidermal cells in dauciform roots were greatly elongated in the transverse plane; epidermal cells of parent roots were unmodified. Although structurally distinct, the physiology of dauciform roots in sedges appears to be analogous to that of proteoid roots of Proteaceae and Fabaceae, and hence, dauciform roots would facilitate access to sorbed P and micronutrients from soils of low fertility.

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.

GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems

PubMed Central

Rellán-Álvarez, Rubén; Lobet, Guillaume; Lindner, Heike; Pradier, Pierre-Luc; Sebastian, Jose; Yee, Muh-Ching; Geng, Yu; Trontin, Charlotte; LaRue, Therese; Schrager-Lavelle, Amanda; Haney, Cara H; Nieu, Rita; Maloof, Julin; Vogel, John P; Dinneny, José R

2015-01-01

Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction, and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated-imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that uses luminescence-based reporters to enable studies of root architecture and gene expression patterns in soil-grown, light-shielded roots. We have developed image analysis algorithms that allow the spatial integration of soil properties, gene expression, and root system architecture traits. We propose GLO-Roots as a system that has great utility in presenting environmental stimuli to roots in ways that evoke natural adaptive responses and in providing tools for studying the multi-dimensional nature of such processes. DOI: http://dx.doi.org/10.7554/eLife.07597.001 PMID:26287479

ROOT.NET: Using ROOT from .NET languages like C# and F#

NASA Astrophysics Data System (ADS)

Watts, G.

2012-12-01

ROOT.NET provides an interface between Microsoft's Common Language Runtime (CLR) and .NET technology and the ubiquitous particle physics analysis tool, ROOT. ROOT.NET automatically generates a series of efficient wrappers around the ROOT API. Unlike pyROOT, these wrappers are statically typed and so are highly efficient as compared to the Python wrappers. The connection to .NET means that one gains access to the full series of languages developed for the CLR including functional languages like F# (based on OCaml). Many features that make ROOT objects work well in the .NET world are added (properties, IEnumerable interface, LINQ compatibility, etc.). Dynamic languages based on the CLR can be used as well, of course (Python, for example). Additionally it is now possible to access ROOT objects that are unknown to the translation tool. This poster will describe the techniques used to effect this translation, along with performance comparisons, and examples. All described source code is posted on the open source site CodePlex.

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

Characterization of Pearl Millet Root Architecture and Anatomy Reveals Three Types of Lateral Roots

PubMed Central

Passot, Sixtine; Gnacko, Fatoumata; Moukouanga, Daniel; Lucas, Mikaël; Guyomarc’h, Soazig; Ortega, Beatriz Moreno; Atkinson, Jonathan A.; Belko, Marème N.; Bennett, Malcolm J.; Gantet, Pascal; Wells, Darren M.; Guédon, Yann; Vigouroux, Yves; Verdeil, Jean-Luc; Muller, Bertrand; Laplaze, Laurent

2016-01-01

Pearl millet plays an important role for food security in arid regions of Africa and India. Nevertheless, it is considered an orphan crop as it lags far behind other cereals in terms of genetic improvement efforts. Breeding pearl millet varieties with improved root traits promises to deliver benefits in water and nutrient acquisition. Here, we characterize early pearl millet root system development using several different root phenotyping approaches that include rhizotrons and microCT. We report that early stage pearl millet root system development is characterized by a fast growing primary root that quickly colonizes deeper soil horizons. We also describe root anatomical studies that revealed three distinct types of lateral roots that form on both primary roots and crown roots. Finally, we detected significant variation for two root architectural traits, primary root lenght and lateral root density, in pearl millet inbred lines. This study provides the basis for subsequent genetic experiments to identify loci associated with interesting early root development traits in this important cereal. PMID:27379124

A new Approach for Quantifying Root-Reinforcement of Streambanks: the RipRoot Model

NASA Astrophysics Data System (ADS)

Pollen, N. L.; Simon, A.

2003-12-01

Riparian vegetation plays an important role in controlling geotechnical and fluvial processes acting along and within streambanks through the binding effects of roots. Quantification of this mechanical effect is therefore essential to accurately model streambank stability. Until now, most attempts to include the effects of root reinforcement by riparian vegetation have used root-cohesion values estimated using the Wu et al. (1979) equation, requiring the tensile strengths and diameters of the roots crossing the potential shear-plane. However, the Wu et al. equation is a static model that assumes that all roots break, and that they all break simultaneously. Field observations and laboratory experiments have shown that in reality the roots do not all break simultaneously, and that the breaking of roots during mass failure is in fact a dynamic process. Static models such as the Wu et al. equation are therefore likely to produce overestimations of cohesion due to roots. As a response to this concern, a dynamic root reinforcement model (RipRoot) was developed, based on the concepts of fiber bundle models (FBM's) used in materials science. Within the model the root-soil system is loaded incrementally resulting in progressive root breaking and redistribution of stresses from the broken roots to the remaining intact roots in the soil matrix. The redistribution and loading process continues until either all of the roots have broken, or equilibrium is reached where the root network supports the driving force imposed on the bank. The increase in bank cohesion using the static Wu et al. equation are 18% to 38% higher than RipRoot for riparian tree species, including Black Willow, Sandbar Willow, Cottonwood, River Birch and Eastern Sycamore, and 49% higher for Switch Grass. These variations in cohesion values can have a significant impact on streambank Factor of Safety (Fs) values calculated using the Simon et al. (2000) bank-stability model. For example, a 3m high silt

Resistance to compression of weakened roots subjected to different root reconstruction protocols

PubMed Central

ZOGHEIB, Lucas Villaça; SAAVEDRA, Guilherme de Siqueira Ferreira Anzaloni; CARDOSO, Paula Elaine; VALERA, Márcia Carneiro; de ARAÚJO, Maria Amélia Máximo

2011-01-01

Objective This study evaluated, in vitro, the fracture resistance of human non-vital teeth restored with different reconstruction protocols. Material and methods Forty human anterior roots of similar shape and dimensions were assigned to four groups (n=10), according to the root reconstruction protocol: Group I (control): non-weakened roots with glass fiber post; Group II: roots with composite resin by incremental technique and glass fiber post; Group III: roots with accessory glass fiber posts and glass fiber post; and Group IV: roots with anatomic glass fiber post technique. Following post cementation and core reconstruction, the roots were embedded in chemically activated acrylic resin and submitted to fracture resistance testing, with a compressive load at an angle of 45º in relation to the long axis of the root at a speed of 0.5 mm/min until fracture. All data were statistically analyzed with bilateral Dunnett's test (α=0.05). Results Group I presented higher mean values of fracture resistance when compared with the three experimental groups, which, in turn, presented similar resistance to fracture among each other. None of the techniques of root reconstruction with intraradicular posts improved root strength, and the incremental technique was suggested as being the most recommendable, since the type of fracture that occurred allowed the remaining dental structure to be repaired. Conclusion The results of this in vitro study suggest that the healthy remaining radicular dentin is more important to increase fracture resistance than the root reconstruction protocol. PMID:22231002

Root and Root Canal Morphology of Human Third Molar Teeth.

PubMed

Mohammadi, Zahed; Jafarzadeh, Hamid; Shalavi, Sousan; Bandi, Shilpa; Patil, Shankargouda

2015-04-01

Successful root canal treatment depends on having comprehensive information regarding the root(s)/canal(s) anatomy. Dentists may have some complication in treatment of third molars because the difficulty in their access, their aberrant occlusal anatomy and different patterns of eruption. The aim of this review was to review and address the number of roots and root canals in third molars, prevalence of confluent canals in third molars, C-shaped canals, dilaceration and fusion in third molars, autotransplantation of third molars and endodontic treatment strategies for third molars.

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...

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...

Effect of different root canal sealers on fracture strength of simulated immature roots.

PubMed

Ulusoy, Özgür İlke Atasoy; Nayır, Yelda; Darendeliler-Yaman, Sis

2011-10-01

The objective of this study was to compare the effects of different root canal sealers on fracture resistance of simulated immature teeth. One hundred eight roots were divided into 9 groups. The roots were instrumented except the negative controls. Four millimeters of mineral trioxide aggregate (MTA) barriers were placed apically. The roots were backfilled as follows: group 1, AH Plus+gutta-percha; group 2, EndoREZ+gutta-percha; group 3, EndoREZ+Resilon; group 4, Hybrid Root SEAL+gutta-percha; group 5, Hybrid Root SEAL+Resilon; group 6, iRootSP+gutta-percha; group 7, iRootSP+Resilon; group 8, No obturation other than MTA barrier; group 9, No instrumentation, no obturation. A compressive loading was applied at a speed of 1 mm/min. Data were compared with ANOVA and Duncan tests. Group 5 showed the highest resistance to fracture. The fracture values of group 3 were lower than those of the other experimental groups. Hybrid Root SEAL and iRootSP reinforce the simulated immature roots against fracture when used with either gutta-percha or Resilon. Copyright © 2011 Mosby, Inc. All rights reserved.

Lateral root initiation in Marsilea quadrifolia. I. Origin and histogensis of lateral roots

NASA Technical Reports Server (NTRS)

Lin, B. L.; Raghavan, V.

1991-01-01

In Marsilea quadrifolia, lateral roots arise from modified single cells of the endodermis located opposite the protoxylem poles within the meristematic region of the parent root. The initial cell divides in four specific planes to establish a five-celled lateral root primordium, with a tetrahedral apical cell in the centre and the oldest merophytes and the root cap along the sides. The cells of the merophyte divide in a precise pattern to give rise to the cells of the cortex, endodermis, pericycle, and vascular tissues of the emerging lateral root. Although the construction of the parent root is more complicated than that of lateral roots, patterns of cell division and tissue formation are similar in both types of roots, with the various tissues being arranged in similar positions in relation to the central axis. Vascular connection between the lateral root primordium and the parent root is derived from the pericycle cells lying between the former and the protoxylem members of the latter. It is proposed that the central axis of the root is not only a geometric centre, but also a physiological centre which determines the fate of the different cell types.

[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.

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

Implementing Dynamic Root Optimization in Noah-MP for Simulating Phreatophytic Root Water Uptake

NASA Astrophysics Data System (ADS)

Wang, Ping; Niu, Guo-Yue; Fang, Yuan-Hao; Wu, Run-Jian; Yu, Jing-Jie; Yuan, Guo-Fu; Pozdniakov, Sergey P.; Scott, Russell L.

2018-03-01

Widely distributed in arid and semiarid regions, phreatophytic roots extend into the saturated zone and extract water directly from groundwater. In this paper, we implemented a vegetation optimality model of root dynamics (VOM-ROOT) in the Noah land surface model with multiparameterization options (Noah-MP LSM) to model the extraction of groundwater through phreatophytic roots at a riparian site with a hyperarid climate (with precipitation of 35 mm/yr) in northwestern China. VOM-ROOT numerically describes the natural optimization of the root profile in response to changes in subsurface water conditions. The coupled Noah-MP/VOM-ROOT model substantially improves the simulation of surface energy and water fluxes, particularly during the growing season, compared to the prescribed static root profile in the default Noah-MP. In the coupled model, more roots are required to grow into the saturated zone to meet transpiration demand when the groundwater level declines over the growing season. The modeling results indicate that at the study site, the modeled annual transpiration is 472 mm, accounting for 92.3% of the total evapotranspiration. Direct root water uptake from the capillary fringe and groundwater, which is supplied by lateral groundwater flow, accounts for approximately 84% of the total transpiration. This study demonstrates the importance of implementing a dynamic root scheme in a land surface model for adequately simulating phreatophytic root water uptake and the associated latent heat flux.

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

Simulating Macrosegregation in Var Ingots of Titanium Alloy During Solidification

DTIC Science & Technology

2006-06-01

spacings in Ti- 6Al - 4V were estimated. A summary-status of the use of software by VAR titanium -ingot producers in the USA is also given. In its...Ti- 6Al - 4V with a melting condition provided by RMI Titanium Company (Proposed Case 11). Two ingots are simulated; one is simulated assuming a...revealed a more intense band. Since primary arm spacings in titanium alloys are not available, primary dendrite arm spacings in Ti-6A1- 4V were

Hydraulic conductivity of soil-grown lupine and maize unbranched roots and maize root-shoot junctions.

PubMed

Meunier, Félicien; Zarebanadkouki, Mohsen; Ahmed, Mutez A; Carminati, Andrea; Couvreur, Valentin; Javaux, Mathieu

2018-01-26

Improving or maintaining crop productivity under conditions of long term change of soil water availability and atmosphere demand for water is one the big challenges of this century. It requires a deep understanding of crop water acquisition properties, i.e. root system architecture and root hydraulic properties among other characteristics of the soil-plant-atmosphere continuum. A root pressure probe technique was used to measure the root hydraulic conductances of seven-week old maize and lupine plants grown in sandy soil. Unbranched root segments were excised in lateral, seminal, crown and brace roots of maize, and in lateral roots of lupine. Their total hydraulic conductance was quantified under steady-state hydrostatic gradient for progressively shorter segments. Furthermore, the axial conductance of proximal root regions removed at each step of root shortening was measured as well. Analytical solutions of the water flow equations in unbranched roots developed recently and relating root total conductance profiles to axial and radial conductivities were used to retrieve the root radial hydraulic conductivity profile along each root type, and quantify its uncertainty. Interestingly, the optimized root radial conductivities and measured axial conductances displayed significant differences across root types and species. However, the measured root total conductances did not differ significantly. As compared to measurements reported in the literature, our axial and radial conductivities concentrate in the lower range of herbaceous species hydraulic properties. In a final experiment, the hydraulic conductances of root junctions to maize stem were observed to highly depend on root type. Surprisingly maize brace root junctions were an order of magnitude more conductive than the other crown and seminal roots, suggesting potential regulation mechanism for root water uptake location and a potential role of the maize brace roots for water uptake more important than reported

1D-VAR Retrieval Using Superchannels

NASA Technical Reports Server (NTRS)

Liu, Xu; Zhou, Daniel; Larar, Allen; Smith, William L.; Schluessel, Peter; Mango, Stephen; SaintGermain, Karen

2008-01-01

Since modern ultra-spectral remote sensors have thousands of channels, it is difficult to include all of them in a 1D-var retrieval system. We will describe a physical inversion algorithm, which includes all available channels for the atmospheric temperature, moisture, cloud, and surface parameter retrievals. Both the forward model and the inversion algorithm compress the channel radiances into super channels. These super channels are obtained by projecting the radiance spectra onto a set of pre-calculated eigenvectors. The forward model provides both super channel properties and jacobian in EOF space directly. For ultra-spectral sensors such as Infrared Atmospheric Sounding Interferometer (IASI) and the NPOESS Airborne Sounder Testbed Interferometer (NAST), a compression ratio of more than 80 can be achieved, leading to a significant reduction in computations involved in an inversion process. Results will be shown applying the algorithm to real IASI and NAST data.

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

Role of Root Hairs and Lateral Roots in Silicon Uptake by Rice

PubMed Central

Ma, Jian Feng; Goto, Shoko; Tamai, Kazunori; Ichii, Masahiko

2001-01-01

The rice plant (Oryza sativa L. cv Oochikara) is known to be a Si accumulator, but the mechanism responsible for the high uptake of Si by the roots is not well understood. We investigated the role of root hairs and lateral roots in the Si uptake using two mutants of rice, one defective in the formation of root hairs (RH2) and another in that of lateral roots (RM109). Uptake experiments with nutrient solution during both a short term (up to 12 h) and relatively long term (26 d) showed that there was no significant difference in Si uptake between RH2 and the wild type (WT), whereas the Si uptake of RM109 was much less than that of WT. The number of silica bodies formed on the third leaf in RH2 was similar to that in WT, but the number of silica bodies in RM109 was only 40% of that in WT, when grown in soil amended with Si under flooded conditions. There was also no difference in the shoot Si concentration between WT and RH2 when grown in soil under upland conditions. Using a multi-compartment transport box, the Si uptake at the root tip (0–1 cm, without lateral roots and root hairs) was found to be similar in WT, RH2, and RM109. However, the Si uptake in the mature zone (1–4 cm from root tip) was significantly lower in RM109 than in WT, whereas no difference was found in Si uptake between WT and RH2. All these results clearly indicate that lateral roots contribute to the Si uptake in rice plant, whereas root hairs do not. Analysis of F2 populations between RM109 and WT showed that Si uptake was correlated with the presence of lateral roots and that the gene controlling formation of lateral roots and Si uptake is a dominant gene. PMID:11743120

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.

[1st environmental isolation of Cryptococcus neoformans var. gattii in Argentina].

PubMed

Davel, G; Abrantes, R; Brudny, M; Córdoba, S; Rodero, L; Canteros, C E; Perrotta, D

2003-01-01

Two strains of C. neoformans var. gattii serotype B were isolated from a park in Buenos Aires city, Argentina. Samples were collected in spring, rubbing with swabs on the inner hollow of Eucalyptus spp. and other trees, which were not identified at the collection moment. Samples were swabbed directly onto cafeic acid with antibiotic agar, then incubated at 28 degrees C and observed daily for a week. Isolates were recovered from cafeic acid medium showing characteristic colonies of the species that allowed differentiation from other microorganisms of the sample. Identification was performed using carbohydrate fermentation, assimilation of nitrogen and carbon sources, and urease and phenoloxidase detection. Strain variety was determined with canavanine-glicine-bromotimol blue agar medium (CGB). Genotypic characterization using AP-PCR with (GACA)4 aleatory primer showed that both band profiles could be differentiated by only one band. These two strains were isolated from tree species different from Eucalyptus spp. These isolates from natural sources demonstrate that C. neoformans var. gattii efosts in Buenos Aires city environment and that it is not necessarily associated with Eucalyptus spp. The presence of C. neoformansvar. gattii in the environment, detected for the first time in Argentina, may explain its sporadic association with human infections in the local population.

Measuring and Modeling Root Distribution and Root Reinforcement in Forested Slopes for Slope Stability Calculations

NASA Astrophysics Data System (ADS)

Cohen, D.; Giadrossich, F.; Schwarz, M.; Vergani, C.

2016-12-01

Roots provide mechanical anchorage and reinforcement of soils on slopes. Roots also modify soil hydrological properties (soil moisture content, pore-water pressure, preferential flow paths) via subsurface flow path associated with root architecture, root density, and root-size distribution. Interactions of root-soil mechanical and hydrological processes are an important control of shallow landslide initiation during rainfall events and slope stability. Knowledge of root-distribution and root strength are key components to estimate slope stability in vegetated slopes and for the management of protection forest in steep mountainous area. We present data that show the importance of measuring root strength directly in the field and present methods for these measurements. These data indicate that the tensile force mobilized in roots depends on root elongation (a function of soil displacement), root size, and on whether roots break in tension of slip out of the soil. Measurements indicate that large lateral roots that cross tension cracks at the scarp are important for slope stability calculations owing to their large tensional resistance. These roots are often overlooked and when included, their strength is overestimated because extrapolated from measurements on small roots. We present planned field experiments that will measure directly the force held by roots of different sizes during the triggering of a shallow landslide by rainfall. These field data are then used in a model of root reinforcement based on fiber-bundle concepts that span different spacial scales, from a single root to the stand scale, and different time scales, from timber harvest to root decay. This model computes the strength of root bundles in tension and in compression and their effect on soil strength. Up-scaled to the stand the model yields the distribution of root reinforcement as a function of tree density, distance from tree, tree species and age with the objective of providing quantitative

Aberrant meiotic behavior in Agave tequilana Weber var. azul

PubMed Central

Ruvalcaba-Ruiz, Domingo; Rodríguez-Garay, Benjamin

2002-01-01

Background Agave tequilana Weber var. azul, is the only one variety permitted by federal law in México to be used for tequila production which is the most popular contemporary alcoholic beverage made from agave and recognized worldwide. Despite the economic, genetic, and ornamental value of the plant, it has not been subjected to detailed cytogenetic research, which could lead to a better understanding of its reproduction for future genetic improvement. The objective of this work was to study the meiotic behavior in pollen mother cells and its implications on the pollen viability in Agave tequilana Weber var. azul. Results The analysis of Pollen Mother Cells in anaphase I (A-I) showed 82.56% of cells with a normal anaphase and, 17.44% with an irregular anaphase. In which 5.28% corresponded to cells with side arm bridges (SAB); 3.68% cells with one bridge and one fragment; 2.58% of irregular anaphase showed cells with one or two lagging chromosomes and 2.95% showed one acentric fragment; cells with two bridges and cells with two bridges and one acentric fragment were observed in frequencies of 1.60% and 1.35% respectively. In anaphase II some cells showed bridges and fragments too. Aberrant A-I cells had many shrunken or empty pollen grains (42.00%) and 58.00 % viable pollen. Conclusion The observed meiotic irregularities suggest that structural chromosome aberrations have occurred, such as heterozygous inversions, sister chromatid exchanges, deletions and duplications which in turn are reflected in a low pollen viability. PMID:12396234

Aberrant meiotic behavior in Agave tequilana Weber var. azul.

PubMed

Ruvalcaba-Ruiz, Domingo; Rodríguez-Garay, Benjamin

2002-10-23

Agave tequilana Weber var. azul, is the only one variety permitted by federal law in México to be used for tequila production which is the most popular contemporary alcoholic beverage made from agave and recognized worldwide. Despite the economic, genetic, and ornamental value of the plant, it has not been subjected to detailed cytogenetic research, which could lead to a better understanding of its reproduction for future genetic improvement. The objective of this work was to study the meiotic behavior in pollen mother cells and its implications on the pollen viability in Agave tequilana Weber var. azul. The analysis of Pollen Mother Cells in anaphase I (A-I) showed 82.56% of cells with a normal anaphase and, 17.44% with an irregular anaphase. In which 5.28% corresponded to cells with side arm bridges (SAB); 3.68% cells with one bridge and one fragment; 2.58% of irregular anaphase showed cells with one or two lagging chromosomes and 2.95% showed one acentric fragment; cells with two bridges and cells with two bridges and one acentric fragment were observed in frequencies of 1.60% and 1.35% respectively. In anaphase II some cells showed bridges and fragments too. Aberrant A-I cells had many shrunken or empty pollen grains (42.00%) and 58.00 % viable pollen. The observed meiotic irregularities suggest that structural chromosome aberrations have occurred, such as heterozygous inversions, sister chromatid exchanges, deletions and duplications which in turn are reflected in a low pollen viability.

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.

GiA Roots: software for the high throughput analysis of plant root system architecture.

PubMed

Galkovskyi, Taras; Mileyko, Yuriy; Bucksch, Alexander; Moore, Brad; Symonova, Olga; Price, Charles A; Topp, Christopher N; Iyer-Pascuzzi, Anjali S; Zurek, Paul R; Fang, Suqin; Harer, John; Benfey, Philip N; Weitz, Joshua S

2012-07-26

Characterizing root system architecture (RSA) is essential to understanding the development and function of vascular plants. Identifying RSA-associated genes also represents an underexplored opportunity for crop improvement. Software tools are needed to accelerate the pace at which quantitative traits of RSA are estimated from images of root networks. We have developed GiA Roots (General Image Analysis of Roots), a semi-automated software tool designed specifically for the high-throughput analysis of root system images. GiA Roots includes user-assisted algorithms to distinguish root from background and a fully automated pipeline that extracts dozens of root system phenotypes. Quantitative information on each phenotype, along with intermediate steps for full reproducibility, is returned to the end-user for downstream analysis. GiA Roots has a GUI front end and a command-line interface for interweaving the software into large-scale workflows. GiA Roots can also be extended to estimate novel phenotypes specified by the end-user. We demonstrate the use of GiA Roots on a set of 2393 images of rice roots representing 12 genotypes from the species Oryza sativa. We validate trait measurements against prior analyses of this image set that demonstrated that RSA traits are likely heritable and associated with genotypic differences. Moreover, we demonstrate that GiA Roots is extensible and an end-user can add functionality so that GiA Roots can estimate novel RSA traits. In summary, we show that the software can function as an efficient tool as part of a workflow to move from large numbers of root images to downstream analysis.

Rooting depth and root depth distribution of Trifolium repens × T. uniflorum interspecific hybrids.

PubMed

Nichols, S N; Hofmann, R W; Williams, W M; van Koten, C

2016-05-20

Traits related to root depth distribution were examined in Trifolium repens × T. uniflorum backcross 1 (BC 1 ) hybrids to determine whether root characteristics of white clover could be improved by interspecific hybridization. Two white clover cultivars, two T. uniflorum accessions and two BC 1 populations were grown in 1 -m deep tubes of sand culture. Maximum rooting depth and root mass distribution were measured at four harvests over time, and root distribution data were fitted with a regression model to provide measures of root system shape. Morphological traits were measured at two depths at harvest 3. Root system shape of the hybrids was more similar to T. uniflorum than to white clover. The hybrids and T. uniflorum had a higher rate of decrease in root mass with depth than white clover, which would result in higher proportions of root mass in the upper profile. Percentage total root mass at 100-200 mm depth was higher for T. uniflorum than white clover, and for Crusader BC 1 than 'Crusader'. Roots of the hybrids and T. uniflorum also penetrated deeper than those of white clover. T. uniflorum had thicker roots at 50-100 mm deep than the other entries, and more of its fine root mass at 400-500 mm. The hybrids and white clover had more of their fine root mass higher in the profile. Consequently, T. uniflorum had a higher root length density at 400-500 mm than most entries, and a smaller decrease in root length density with depth. These results demonstrate that rooting characteristics of white clover can be altered by hybridization with T. uniflorum, potentially improving water and nutrient acquisition and drought resistance. Root traits of T. uniflorum are likely to be adaptations to soil moisture and fertility in its natural environment. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Rooting depth and root depth distribution of Trifolium repens × T. uniflorum interspecific hybrids

PubMed Central

Nichols, S. N.; Hofmann, R. W.; Williams, W. M.; van Koten, C.

2016-01-01

Background and aims Traits related to root depth distribution were examined in Trifolium repens × T. uniflorum backcross 1 (BC1) hybrids to determine whether root characteristics of white clover could be improved by interspecific hybridization. Methods Two white clover cultivars, two T. uniflorum accessions and two BC1 populations were grown in 1 -m deep tubes of sand culture. Maximum rooting depth and root mass distribution were measured at four harvests over time, and root distribution data were fitted with a regression model to provide measures of root system shape. Morphological traits were measured at two depths at harvest 3. Key Results Root system shape of the hybrids was more similar to T. uniflorum than to white clover. The hybrids and T. uniflorum had a higher rate of decrease in root mass with depth than white clover, which would result in higher proportions of root mass in the upper profile. Percentage total root mass at 100–200 mm depth was higher for T. uniflorum than white clover, and for Crusader BC1 than ‘Crusader’. Roots of the hybrids and T. uniflorum also penetrated deeper than those of white clover. T. uniflorum had thicker roots at 50–100 mm deep than the other entries, and more of its fine root mass at 400–500 mm. The hybrids and white clover had more of their fine root mass higher in the profile. Consequently, T. uniflorum had a higher root length density at 400–500 mm than most entries, and a smaller decrease in root length density with depth. Conclusions These results demonstrate that rooting characteristics of white clover can be altered by hybridization with T. uniflorum, potentially improving water and nutrient acquisition and drought resistance. Root traits of T. uniflorum are likely to be adaptations to soil moisture and fertility in its natural environment. PMID:27208735

Cadmium translocation by contractile roots differs from that in regular, non-contractile roots

PubMed Central

Lux, Alexander; Lackovič, Andrej; Van Staden, Johannes; Lišková, Desana; Kohanová, Jana; Martinka, Michal

2015-01-01

Background and Aims Contractile roots are known and studied mainly in connection with the process of shrinkage of their basal parts, which acts to pull the shoot of the plant deeper into the ground. Previous studies have shown that the specific structure of these roots results in more intensive water uptake at the base, which is in contrast to regular root types. The purpose of this study was to find out whether the basal parts of contractile roots are also more active in translocation of cadmium to the shoot. Methods Plants of the South African ornamental species Tritonia gladiolaris were cultivated in vitro for 2 months, at which point they possessed well-developed contractile roots. They were then transferred to Petri dishes with horizontally separated compartments of agar containing 50 µmol Cd(NO3)2 in the region of the root base or the root apex. Seedlings of 4-d-old maize (Zea mays) plants, which do not possess contractile roots, were also transferred to similar Petri dishes. The concentrations of Cd in the leaves of the plants were compared after 10 d of cultivation. Anatomical analyses of Tritonia roots were performed using appropriately stained freehand cross-sections. Key Results The process of contraction required specific anatomical adaptation of the root base in Tritonia, with less lignified and less suberized tissues in comparison with the subapical part of the root. These unusual developmental characteristics were accompanied by more intensive translocation of Cd ions from the basal part of contractile roots to the leaves than from the apical–subapical root parts. The opposite effects were seen in the non-contractile roots of maize, with higher uptake and transport by the apical parts of the root and lower uptake and transport by the basal part. Conclusions The specific characteristics of contractile roots may have a significant impact on the uptake of ions, including toxic metals from the soil surface layers. This may be important for plant

Corky root rot

USDA-ARS?s Scientific Manuscript database

Corky root rot (corchosis) was first reported in Argentina in 1985, but the disease was presumably present long before that. The disease occurs in most alfalfa-growing areas of Argentina but is more common in older stands. In space-planted alfalfa trials scored for root problems, corky root rot was ...

Armillaria root rot

USDA-ARS?s Scientific Manuscript database

First described on grapevines in California in the 1880s, Armillaria root rot occurs in all major grape-growing regions of the state. The causal fungus, Armillaria mellea, infects woody grapevine roots and the base of the trunk (the root collar), resulting in a slow decline and eventual death of the...

[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.

The complete chloroplast genome of Capsicum annuum var. glabriusculum using Illumina sequencing.

PubMed

Raveendar, Sebastin; Na, Young-Wang; Lee, Jung-Ro; Shim, Donghwan; Ma, Kyung-Ho; Lee, Sok-Young; Chung, Jong-Wook

2015-07-20

Chloroplast (cp) genome sequences provide a valuable source for DNA barcoding. Molecular phylogenetic studies have concentrated on DNA sequencing of conserved gene loci. However, this approach is time consuming and more difficult to implement when gene organization differs among species. Here we report the complete re-sequencing of the cp genome of Capsicum pepper (Capsicum annuum var. glabriusculum) using the Illumina platform. The total length of the cp genome is 156,817 bp with a 37.7% overall GC content. A pair of inverted repeats (IRs) of 50,284 bp were separated by a small single copy (SSC; 18,948 bp) and a large single copy (LSC; 87,446 bp). The number of cp genes in C. annuum var. glabriusculum is the same as that in other Capsicum species. Variations in the lengths of LSC; SSC and IR regions were the main contributors to the size variation in the cp genome of this species. A total of 125 simple sequence repeat (SSR) and 48 insertions or deletions variants were found by sequence alignment of Capsicum cp genome. These findings provide a foundation for further investigation of cp genome evolution in Capsicum and other higher plants.

Abscisic Acid Regulates Auxin Homeostasis in Rice Root Tips to Promote Root Hair Elongation

PubMed Central

Wang, Tao; Li, Chengxiang; Wu, Zhihua; Jia, Yancui; Wang, Hong; Sun, Shiyong; Mao, Chuanzao; Wang, Xuelu

2017-01-01

Abscisic acid (ABA) plays an essential role in root hair elongation in plants, but the regulatory mechanism remains to be elucidated. In this study, we found that exogenous ABA can promote rice root hair elongation. Transgenic rice overexpressing SAPK10 (Stress/ABA-activated protein kinase 10) had longer root hairs; rice plants overexpressing OsABIL2 (OsABI-Like 2) had attenuated ABA signaling and shorter root hairs, suggesting that the effect of ABA on root hair elongation depends on the conserved PYR/PP2C/SnRK2 ABA signaling module. Treatment of the DR5-GUS and OsPIN-GUS lines with ABA and an auxin efflux inhibitor showed that ABA-induced root hair elongation depends on polar auxin transport. To examine the transcriptional response to ABA, we divided rice root tips into three regions: short root hair, long root hair and root tip zones; and conducted RNA-seq analysis with or without ABA treatment. Examination of genes involved in auxin transport, biosynthesis and metabolism indicated that ABA promotes auxin biosynthesis and polar auxin transport in the root tip, which may lead to auxin accumulation in the long root hair zone. Our findings shed light on how ABA regulates root hair elongation through crosstalk with auxin biosynthesis and transport to orchestrate plant development. PMID:28702040

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(♂).

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

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...

[Effects nutrients on the seedlings root hair development and root growth of Poncirus trifoliata under hydroponics condition].

PubMed

Cao, Xiu; Xia, Ren-Xue; Zhang, De-Jian; Shu, Bo

2013-06-01

Ahydroponics experiment was conducted to study the effects of nutrients (N, P, K, Ca, Mg, Fe, and Mn) deficiency on the length of primary root, the number of lateral roots, and the root hair density, length, and diameter on the primary root and lateral roots of Poncirus trifoliata seedlings. Under the deficiency of each test nutrient, root hair could generate, but was mainly concentrated on the root base and fewer on the root tip. The root hair density on lateral roots was significantly larger than that on primary root, but the root hair length was in adverse. The deficiency of each test nutrient had greater effects on the growth and development of root hairs, with the root hair density on primary root varied from 55.0 to 174.3 mm(-2). As compared with the control, Ca deficiency induced the significant increase of root hair density and length on primary root, P deficiency promoted the root hair density and length on the base and middle part of primary root and on the lateral roots significantly, Fe deficiency increased the root hair density but decreased the root hair length on the tip of primary root significantly, K deficiency significantly decreased the root hair density, length, and diameter on primary root and lateral roots, whereas Mg deficiency increased the root hair length of primary root significantly. In all treatments of nutrient deficiency, the primary root had the similar growth rate, but, with the exceptions of N and Mg deficiency, the lateral roots exhibited shedding and regeneration.

Bioinformatics analysis of the ς-carotene desaturase gene in cabbage (Brassica oleracea var. capitata)

NASA Astrophysics Data System (ADS)

Sun, Bo; Zheng, Aihong; Jiang, Min; Xue, Shengling; Zhang, Fen; Tang, Haoru

2018-04-01

ς-carotene desaturase (ZDS) is an important enzyme in carotenoid biosynthesis. Here, the Brassica oleracea var. capitata ZDS (BocZDS) gene sequences were obtained from Brassica database (BRAD), and preformed for bioinformatics analysis. The BocZDS gene mapped to Scaffold000363, and contains an open reading frame of 1,686 bp that encodes a 561-amino acid protein with a calculated molecular mass of 62.00 kD and an isoelectric point (pI) of 8.2. Subcellular localization predicted the BocZDS gene was in the chloroplast. The conserved domain of the BocZDS protein is PLN02487, indicating that it belongs the member of zeta-carotene desaturase. Homology analysis indicates that the ZDS protein is apparently conserved during plant evolution and is most closely related to B. oleracea var. oleracea, B. napus, and B. rapa. The findings of the present study provide a molecular basis for the elucidation of ZDS gene function in cabbage.

Root morphology and mycorrhizal type strongly influence root production in nutrient hot spots of mixed forests

DOE PAGES

Chen, Weile; Koide, Roger T.; Eissenstat, David M.

2017-04-26

Plants compete for nutrients using a range of strategies. We investigated nutrient foraging within nutrient hot-spots simultaneously available to plant species with diverse root traits. We hypothesized that there would be more root proliferation by thin-root species than by thick-root species, and that root proliferation by thin-root species would limit root proliferation by thick-root species. We conducted a root ingrowth experiment in a temperate forest in eastern USA where root systems of different tree species could interact. Tree species varied in the thickness of their absorptive roots, and were associated with either ectomycorrhizal (EM) or arbuscular mycorrhizal (AM) fungi. Thus,more » there were thin- and thick-root AM and thin- and thick-root EM plant functional groups. Half the ingrowth cores were amended with organic nutrients (dried green leaves). Relative root length abundance, the proportion of total root length in a given soil volume occupied by a particular plant functional group, was calculated for the original root population and ingrowth roots after 6 months. The shift in relative root length abundance from original to ingrowth roots was positive in thin-root species but negative in thick-root species (p < .001), especially in unamended patches (AM: +6% vs. -7%; EM: +8% vs. -9%). Being thin-rooted may thus allow a species to more rapidly recolonize soil after a disturbance, which may influence competition for nutrients. Moreover, we observed that nutrient additions amplified the shift in root length abundance of thin over thick roots in AM trees (+13% vs. -14%), but not in EM trees (+1% vs -3%). In contrast, phospholipid fatty acid biomarkers suggested that EM fungal hyphae strongly proliferated in nutrient hot-spots whereas AM fungal hyphae exhibited only modest proliferation. We found no evidence that when growing in the shared patch, the proliferation of thin roots inhibited the growth of thick roots. As a result, knowledge of root

Root morphology and mycorrhizal type strongly influence root production in nutrient hot spots of mixed forests

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

Chen, Weile; Koide, Roger T.; Eissenstat, David M.

Plants compete for nutrients using a range of strategies. We investigated nutrient foraging within nutrient hot-spots simultaneously available to plant species with diverse root traits. We hypothesized that there would be more root proliferation by thin-root species than by thick-root species, and that root proliferation by thin-root species would limit root proliferation by thick-root species. We conducted a root ingrowth experiment in a temperate forest in eastern USA where root systems of different tree species could interact. Tree species varied in the thickness of their absorptive roots, and were associated with either ectomycorrhizal (EM) or arbuscular mycorrhizal (AM) fungi. Thus,more » there were thin- and thick-root AM and thin- and thick-root EM plant functional groups. Half the ingrowth cores were amended with organic nutrients (dried green leaves). Relative root length abundance, the proportion of total root length in a given soil volume occupied by a particular plant functional group, was calculated for the original root population and ingrowth roots after 6 months. The shift in relative root length abundance from original to ingrowth roots was positive in thin-root species but negative in thick-root species (p < .001), especially in unamended patches (AM: +6% vs. -7%; EM: +8% vs. -9%). Being thin-rooted may thus allow a species to more rapidly recolonize soil after a disturbance, which may influence competition for nutrients. Moreover, we observed that nutrient additions amplified the shift in root length abundance of thin over thick roots in AM trees (+13% vs. -14%), but not in EM trees (+1% vs -3%). In contrast, phospholipid fatty acid biomarkers suggested that EM fungal hyphae strongly proliferated in nutrient hot-spots whereas AM fungal hyphae exhibited only modest proliferation. We found no evidence that when growing in the shared patch, the proliferation of thin roots inhibited the growth of thick roots. As a result, knowledge of root

RootScan: Software for high-throughput analysis of root anatomical traits

USDA-ARS?s Scientific Manuscript database

RootScan is a program for semi-automated image analysis of anatomical phenes in root cross-sections. RootScan uses pixel value thresholds to separate the cross-section from its background and to visually dissect it into tissue regions. Area measurements and object counts are performed within various...

Getting to the roots of it: Genetic and hormonal control of root architecture

PubMed Central

Jung, Janelle K. H.; McCouch, Susan

2013-01-01

Root system architecture (RSA) – the spatial configuration of a root system – is an important developmental and agronomic trait, with implications for overall plant architecture, growth rate and yield, abiotic stress resistance, nutrient uptake, and developmental plasticity in response to environmental changes. Root architecture is modulated by intrinsic, hormone-mediated pathways, intersecting with pathways that perceive and respond to external, environmental signals. The recent development of several non-invasive 2D and 3D root imaging systems has enhanced our ability to accurately observe and quantify architectural traits on complex whole-root systems. Coupled with the powerful marker-based genotyping and sequencing platforms currently available, these root phenotyping technologies lend themselves to large-scale genome-wide association studies, and can speed the identification and characterization of the genes and pathways involved in root system development. This capability provides the foundation for examining the contribution of root architectural traits to the performance of crop varieties in diverse environments. This review focuses on our current understanding of the genes and pathways involved in determining RSA in response to both intrinsic and extrinsic (environmental) response pathways, and provides a brief overview of the latest root system phenotyping technologies and their potential impact on elucidating the genetic control of root development in plants. PMID:23785372

Phenolic acids in the flowers of Althaea rosea var. nigra.

PubMed

Dudek, Marlena; Matławska, Irena; Szkudlarek, Maurycy

2006-01-01

Distribution of phenolic acids in the flowers of Althaea rosea var. nigra has been studied by 2D-TLC and HPLC methods. The phenolic acids occurring in these fractions have been identified as ferulic, vanillic, syringic, p-coumaric, p-hydroxybenzoic, p-hydroxyphenylacetic and caffeic acids. By means of the HPLC methods the contents of major phenolic acids were estimated. From among the phenolic acids analyzed the syringic, p-hydroxybenzoic and p-coumaric acids are dominant. Total content of phenolic acids was determined by the Arnov's method.

Cyanogen Metabolism in Cassava Roots: Impact on Protein Synthesis and Root Development.

PubMed

Zidenga, Tawanda; Siritunga, Dimuth; Sayre, Richard T

2017-01-01

Cassava ( Manihot esculenta Crantz), a staple crop for millions of sub-Saharan Africans, contains high levels of cyanogenic glycosides which protect it against herbivory. However, cyanogens have also been proposed to play a role in nitrogen transport from leaves to roots. Consistent with this hypothesis, analyses of the distribution and activities of enzymes involved in cyanide metabolism provides evidence for cyanide assimilation, derived from linamarin, into amino acids in cassava roots. Both β-cyanoalanine synthase (CAS) and nitrilase (NIT), two enzymes involved in cyanide assimilation to produce asparagine, were observed to have higher activities in roots compared to leaves, consistent with their proposed role in reduced nitrogen assimilation. In addition, rhodanese activity was not detected in cassava roots, indicating that this competing means for cyanide metabolism was not a factor in cyanide detoxification. In contrast, leaves had sufficient rhodanese activity to compete with cyanide assimilation into amino acids. Using transgenic low cyanogen plants, it was shown that reducing root cyanogen levels is associated with elevated root nitrate reductase activity, presumably to compensate for the loss of reduced nitrogen from cyanogens. Finally, we overexpressed Arabidopsis CAS and NIT4 genes in cassava roots to study the feasibility of enhancing root cyanide assimilation into protein. Optimal overexpression of CAS and NIT4 resulted in up to a 50% increase in root total amino acids and a 9% increase in root protein accumulation. However, plant growth and morphology was altered in plants overexpressing these enzymes, demonstrating a complex interaction between cyanide metabolism and hormonal regulation of plant growth.

Cyanogen Metabolism in Cassava Roots: Impact on Protein Synthesis and Root Development

PubMed Central

Zidenga, Tawanda; Siritunga, Dimuth; Sayre, Richard T.

2017-01-01

Cassava (Manihot esculenta Crantz), a staple crop for millions of sub-Saharan Africans, contains high levels of cyanogenic glycosides which protect it against herbivory. However, cyanogens have also been proposed to play a role in nitrogen transport from leaves to roots. Consistent with this hypothesis, analyses of the distribution and activities of enzymes involved in cyanide metabolism provides evidence for cyanide assimilation, derived from linamarin, into amino acids in cassava roots. Both β-cyanoalanine synthase (CAS) and nitrilase (NIT), two enzymes involved in cyanide assimilation to produce asparagine, were observed to have higher activities in roots compared to leaves, consistent with their proposed role in reduced nitrogen assimilation. In addition, rhodanese activity was not detected in cassava roots, indicating that this competing means for cyanide metabolism was not a factor in cyanide detoxification. In contrast, leaves had sufficient rhodanese activity to compete with cyanide assimilation into amino acids. Using transgenic low cyanogen plants, it was shown that reducing root cyanogen levels is associated with elevated root nitrate reductase activity, presumably to compensate for the loss of reduced nitrogen from cyanogens. Finally, we overexpressed Arabidopsis CAS and NIT4 genes in cassava roots to study the feasibility of enhancing root cyanide assimilation into protein. Optimal overexpression of CAS and NIT4 resulted in up to a 50% increase in root total amino acids and a 9% increase in root protein accumulation. However, plant growth and morphology was altered in plants overexpressing these enzymes, demonstrating a complex interaction between cyanide metabolism and hormonal regulation of plant growth. PMID:28286506

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.

Cassava root membrane proteome reveals activities during storage root maturation.

PubMed

Naconsie, Maliwan; Lertpanyasampatha, Manassawe; Viboonjun, Unchera; Netrphan, Supatcharee; Kuwano, Masayoshi; Ogasawara, Naotake; Narangajavana, Jarunya

2016-01-01

Cassava (Manihot esculenta Crantz) is one of the most important crops of Thailand. Its storage roots are used as food, feed, starch production, and be the important source for biofuel and biodegradable plastic production. Despite the importance of cassava storage roots, little is known about the mechanisms involved in their formation. This present study has focused on comparison of the expression profiles of cassava root proteome at various developmental stages using two-dimensional gel electrophoresis and LC-MS/MS. Based on an anatomical study using Toluidine Blue, the secondary growth was confirmed to be essential during the development of cassava storage root. To investigate biochemical processes occurring during storage root maturation, soluble and membrane proteins were isolated from storage roots harvested from 3-, 6-, 9-, and 12-month-old cassava plants. The proteins with differential expression pattern were analysed and identified to be associated with 8 functional groups: protein folding and degradation, energy, metabolism, secondary metabolism, stress response, transport facilitation, cytoskeleton, and unclassified function. The expression profiling of membrane proteins revealed the proteins involved in protein folding and degradation, energy, and cell structure were highly expressed during early stages of development. Integration of these data along with the information available in genome and transcriptome databases is critical to expand knowledge obtained solely from the field of proteomics. Possible role of identified proteins were discussed in relation with the activities during storage root maturation in cassava.

Var C: Long-term photometric and spectral variability of a luminous blue variable in M 33

NASA Astrophysics Data System (ADS)

Burggraf, B.; Weis, K.; Bomans, D. J.; Henze, M.; Meusinger, H.; Sholukhova, O.; Zharova, A.; Pellerin, A.; Becker, A.

2015-09-01

Aims: So far the highly unstable phase of luminous blue variables (LBVs) has not been understood well. It is still uncertain why and which massive stars enter this phase. Investigating the variabilities by looking for a possible regular or even (semi-)periodic behaviour could give a hint at the underlying mechanism for these variations and might answer the question of where these variabilities originate. Finding out more about the LBV phase also means understanding massive stars better in general, which have (e.g. by enriching the ISM with heavy elements, providing ionising radiation and kinetic energy) a strong and significant influence on the ISM, hence also on their host galaxy. Methods: Photometric and spectroscopic data were taken for the LBV Var C in M 33 to investigate its recent status. In addition, scanned historic plates, archival data, and data from the literature were gathered to trace Var C's behaviour in the past. Its long-term variability and periodicity was investigated. Results: Our investigation of the variability indicates possible (semi-)periodic behaviour with a period of 42.3 years for Var C. That Var C's light curve covers a time span of more than 100 years means that more than two full periods of the cycle are visible. The critical historic maximum around 1905 is less strong but discernible even with the currently rare historic data. The semi-periodic and secular structure of the light curve is similar to the one of LMC R71. Both light curves hint at a new aspect in the evolution of LBVs. Based on observations collected at the Thüringer Landessternwarte (TLS) Tautenburg.Based on observations collected at the Centro Astronómico Hispano Alemán (CAHA) at Calar Alto, operated jointly by the Max-Planck Institut für Astronomie and the Instituto de Astrofísica de Andalucía (CSIC).Tables 2-4, and 6 are available in electronic form at http://www.aanda.org

Root system markup language: toward a unified root architecture description language.

PubMed

Lobet, Guillaume; Pound, Michael P; Diener, Julien; Pradal, Christophe; Draye, Xavier; Godin, Christophe; Javaux, Mathieu; Leitner, Daniel; Meunier, Félicien; Nacry, Philippe; Pridmore, Tony P; Schnepf, Andrea

2015-03-01

The number of image analysis tools supporting the extraction of architectural features of root systems has increased in recent years. These tools offer a handy set of complementary facilities, yet it is widely accepted that none of these software tools is able to extract in an efficient way the growing array of static and dynamic features for different types of images and species. We describe the Root System Markup Language (RSML), which has been designed to overcome two major challenges: (1) to enable portability of root architecture data between different software tools in an easy and interoperable manner, allowing seamless collaborative work; and (2) to provide a standard format upon which to base central repositories that will soon arise following the expanding worldwide root phenotyping effort. RSML follows the XML standard to store two- or three-dimensional image metadata, plant and root properties and geometries, continuous functions along individual root paths, and a suite of annotations at the image, plant, or root scale at one or several time points. Plant ontologies are used to describe botanical entities that are relevant at the scale of root system architecture. An XML schema describes the features and constraints of RSML, and open-source packages have been developed in several languages (R, Excel, Java, Python, and C#) to enable researchers to integrate RSML files into popular research workflow. © 2015 American Society of Plant Biologists. All Rights Reserved.

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.

Auxin fluxes in the root apex co-regulate gravitropism and lateral root initiation.

PubMed

Lucas, M; Godin, C; Jay-Allemand, C; Laplaze, L

2008-01-01

Root architecture plays an important role in water and nutrient acquisition and in the ability of the plant to adapt to the soil. Lateral root development is the main determinant of the shape of the root system and is controlled by external factors such as nutrient concentration. Here it is shown that lateral root initiation and root gravitropism, two processes that are regulated by auxin, are co-regulated in Arabidopsis. A mathematical model was generated that can predict the effects of gravistimulations on lateral root initiation density and suggests that lateral root initiation is controlled by an inhibitory fields mechanism. Moreover, gene transactivation experiments suggest a mechanism involving a single auxin transport route for both responses. Finally, co-regulation may offer a selective advantage by optimizing soil exploration as supported by a simple quantitative analysis.

Phene Synergism between Root Hair Length and Basal Root Growth Angle for Phosphorus Acquisition1[OPEN

PubMed Central

Miguel, Magalhaes Amade

2015-01-01

Shallow basal root growth angle (BRGA) increases phosphorus acquisition efficiency by enhancing topsoil foraging because in most soils, phosphorus is concentrated in the topsoil. Root hair length and density (RHL/D) increase phosphorus acquisition by expanding the soil volume subject to phosphorus depletion through diffusion. We hypothesized that shallow BRGA and large RHL/D are synergetic for phosphorus acquisition, meaning that their combined effect is greater than the sum of their individual effects. To evaluate this hypothesis, phosphorus acquisition in the field in Mozambique was compared among recombinant inbred lines of common bean (Phaseolus vulgaris) having four distinct root phenotypes: long root hairs and shallow basal roots, long root hairs and deep basal roots, short root hairs and shallow basal roots, and short root hairs and deep basal roots. The results revealed substantial synergism between BRGA and RHL/D. Compared with short-haired, deep-rooted phenotypes, long root hairs increased shoot biomass under phosphorus stress by 89%, while shallow roots increased shoot biomass by 58%. Genotypes with both long root hairs and shallow roots had 298% greater biomass accumulation than short-haired, deep-rooted phenotypes. Therefore, the utility of shallow basal roots and long root hairs for phosphorus acquisition in combination is twice as large as their additive effects. We conclude that the anatomical phene of long, dense root hairs and the architectural phene of shallower basal root growth are synergetic for phosphorus acquisition. Phene synergism may be common in plant biology and can have substantial importance for plant fitness, as shown here. PMID:25699587

Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions.

PubMed

Uga, Yusaku; Sugimoto, Kazuhiko; Ogawa, Satoshi; Rane, Jagadish; Ishitani, Manabu; Hara, Naho; Kitomi, Yuka; Inukai, Yoshiaki; Ono, Kazuko; Kanno, Noriko; Inoue, Haruhiko; Takehisa, Hinako; Motoyama, Ritsuko; Nagamura, Yoshiaki; Wu, Jianzhong; Matsumoto, Takashi; Takai, Toshiyuki; Okuno, Kazutoshi; Yano, Masahiro

2013-09-01

The genetic improvement of drought resistance is essential for stable and adequate crop production in drought-prone areas. Here we demonstrate that alteration of root system architecture improves drought avoidance through the cloning and characterization of DEEPER ROOTING 1 (DRO1), a rice quantitative trait locus controlling root growth angle. DRO1 is negatively regulated by auxin and is involved in cell elongation in the root tip that causes asymmetric root growth and downward bending of the root in response to gravity. Higher expression of DRO1 increases the root growth angle, whereby roots grow in a more downward direction. Introducing DRO1 into a shallow-rooting rice cultivar by backcrossing enabled the resulting line to avoid drought by increasing deep rooting, which maintained high yield performance under drought conditions relative to the recipient cultivar. Our experiments suggest that control of root system architecture will contribute to drought avoidance in crops.

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).

Molecular structures of fructans from Agave tequilana Weber var. azul.

PubMed

Lopez, Mercedes G; Mancilla-Margalli, Norma A; Mendoza-Diaz, Guillermo

2003-12-31

Agave plants utilize crassulacean acid metabolism (CAM) for CO(2) fixation. Fructans are the principal photosynthetic products generated by agave plants. These carbohydrates are fructose-bound polymers frequently with a single glucose moiety. Agave tequilana Weber var. azul is an economically important CAM species not only because it is the sole plant allowed for tequila production but because it is a potential source of prebiotics. Because of the large amounts of carbohydrates in A. tequilana, in this study the molecular structures of its fructans were determined by fructan derivatization for linkage analysis coupled with gas chromatography-mass spectrometry (GC-MS), nuclear magnetic resonance (NMR), and matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS). Fructans were extracted from 8-year-old A. tequilana plants. The linkage types present in fructans from A. tequilana were determined by permethylation followed by reductive cleavage, acetylation, and finally GC-MS analysis. Analysis of the degree of polymerization (DP) estimated by (1)H NMR integration and (13)C NMR and confirmed by MALDI-TOF-MS showed a wide DP ranging from 3 to 29 units. All of the analyses performed demonstrated that fructans from A. tequilana consist of a complex mixture of fructooligosaccharides containing principally beta(2 --> 1) linkages, but also beta(2 --> 6) and branch moieties were observed. Finally, it can be stated that fructans from A. tequilana Weber var. azul are not an inulin type as previously thought.

SEVIRI 4D-var assimilation analysing the April 2010 Eyjafjallajökull ash dispersion

NASA Astrophysics Data System (ADS)

Lange, Anne Caroline; Elbern, Hendrik

2016-04-01

We present first results of four dimensional variational (4D-var) data assimilation analysis applying SEVIRI observations to the Eulerian regional chemistry and aerosol transport model EURAD-IM (European Air Pollution Dispersion - Inverse Model). Optimising atmospheric dispersion models in terms of volcanic ash transport predictions by observations is especially essential for the aviation industry and associated interests. Remote sensing satellite observations are instrumental for ash detection and monitoring. We choose volcanic ash column retrievals of the Spinning Enhanced Visible and Infrared Imager (SEVIRI) because as infrared instrument on the geostationary satellite Meteosat Second Generation it delivers measurements with high temporal resolution during day and night. The retrieval method relies on the reverse absorption effect. In the framework of the national initiative ESKP (Earth System Knowledge Platform) and the European ACTRIS-2 (Aerosol, Clouds, and Trace gases Research InfraStructure) project, we developed new modules (forward and adjoint) within the EURAD-IM, which are able to process SEVIRI ash column data as observational input to the 4D-var system. The focus of the 4D-var analysis is on initial value optimisation of the volcanic ash clouds that were emitted during the explosive Eyjafjallajökull eruption in April 2010. This eruption caused high public interest because of air traffic closures and it was particularly well observed from many different observation systems all over Europe. Considering multiple observation periods simultaneously in one assimilation window generates a continuous trajectory in the phase space and ensures that past observations are considered within their uncertainties. Results are validated mainly by lidar (LIght Detection And Ranging) observations, both ground and satellite based.

Root type matters: measurements of water uptake by seminal, crown and lateral roots of maize

NASA Astrophysics Data System (ADS)

Ahmed, Mutez Ali; Zarebanadkouki, Mohsen; Kaestner, Anders; Carminati, Andrea

2016-04-01

Roots play a key role in water acquisition and are a significant component of plant adaptation to different environmental conditions. Although maize (Zea mays L.) is one of the most important crops worldwide, there is limited information on the function of different root segments and types in extracting water from soils. Aim of this study was to investigate the location of root water uptake in mature maize. We used neutron radiography to image the spatial distribution of maize roots and trace the transport of injected deuterated water (D2O) in soil and roots. Maize plants were grown in aluminum containers filled with a sandy soil that was kept homogeneously wet throughout the experiment. When the plants were five weeks-old, we injected D2O into selected soil regions. The transport of D2O was simulated using a diffusion-convection numerical model. By fitting the observed D2O transport we quantified the diffusion coefficient and the water uptake of the different root segments. The model was initially developed and tested with two weeks-old maize (Ahmed et. al. 2015), for which we found that water was mainly taken up by lateral roots and the water uptake of the seminal roots was negligible. Here, we used this method to measure root water uptake in a mature maize root system. The root architecture of five weeks-old maize consisted of primary and seminal roots with long laterals and crown (nodal) roots that emerged from the above ground part of the plant two weeks after planting. The crown roots were thicker than the seminal roots and had fewer and shorter laterals. Surprisingly, we found that the water was mainly taken up by the crown roots and their laterals, while the lateral roots of seminal roots, which were the main location of water uptake of younger plants, stopped to take up water. Interestingly, we also found that in contrast to the seminal roots, the crown roots were able to take up water also from their distal segments. We conclude that for the two weeks

Strigolactones Effects on Root Growth

NASA Astrophysics Data System (ADS)

Koltai, Hinanit

2012-07-01

Strigolactones (SLs) were defined as a new group of plant hormones that suppress lateral shoot branching. Our previous studies suggested SLs to be regulators of root development. SLs were shown to alter root architecture by regulating lateral root formation and to affect root hair elongation in Arabidopsis. Another important effect of SLs on root growth was shown to be associated with root directional growth. Supplementation of SLs to roots led to alterations in root directional growth, whereas associated mutants showed asymmetrical root growth, which was influenced by environmental factors. The regulation by SLs of root development was shown to be conducted via a cross talk of SLs with other plant hormones, including auxin. SLs were shown to regulate auxin transport, and to interfere with the activity of auxin-efflux carriers. Therefore, it might be that SLs are regulators of root directional growth as a result of their ability to regulated auxin transport. However, other evidences suggest a localized effect of SLs on cell division, which may not necessarily be associated with auxin efflux. These and other, recent hypothesis as to the SLs mode of action and the associated root perception and response to environmental factors will be discussed.

Plant roots use a patterning mechanism to position lateral root branches toward available water.

PubMed

Bao, Yun; Aggarwal, Pooja; Robbins, Neil E; Sturrock, Craig J; Thompson, Mark C; Tan, Han Qi; Tham, Cliff; Duan, Lina; Rodriguez, Pedro L; Vernoux, Teva; Mooney, Sacha J; Bennett, Malcolm J; Dinneny, José R

2014-06-24

The architecture of the branched root system of plants is a major determinant of vigor. Water availability is known to impact root physiology and growth; however, the spatial scale at which this stimulus influences root architecture is poorly understood. Here we reveal that differences in the availability of water across the circumferential axis of the root create spatial cues that determine the position of lateral root branches. We show that roots of several plant species can distinguish between a wet surface and air environments and that this also impacts the patterning of root hairs, anthocyanins, and aerenchyma in a phenomenon we describe as hydropatterning. This environmental response is distinct from a touch response and requires available water to induce lateral roots along a contacted surface. X-ray microscale computed tomography and 3D reconstruction of soil-grown root systems demonstrate that such responses also occur under physiologically relevant conditions. Using early-stage lateral root markers, we show that hydropatterning acts before the initiation stage and likely determines the circumferential position at which lateral root founder cells are specified. Hydropatterning is independent of endogenous abscisic acid signaling, distinguishing it from a classic water-stress response. Higher water availability induces the biosynthesis and transport of the lateral root-inductive signal auxin through local regulation of tryptophan aminotransferase of Arabidopsis 1 and PIN-formed 3, both of which are necessary for normal hydropatterning. Our work suggests that water availability is sensed and interpreted at the suborgan level and locally patterns a wide variety of developmental processes in the root.

Air lateral root pruning affects longleaf pine seedling root system morphology

Treesearch

Shi-Jean Susana Sung; Dave Haywood

2016-01-01

Longleaf pine (Pinus palustris) seedlings were cultured with air lateral root pruning (side-vented containers, VT) or without (solid-walled containers, SW). Seedling root system morphology and growth were assessed before planting and 8 and 14 months after planting. Although VT seedlings had greater root collar diameter than the SW before planting,...

Coupling root architecture and pore network modeling - an attempt towards better understanding root-soil interactions

NASA Astrophysics Data System (ADS)

Leitner, Daniel; Bodner, Gernot; Raoof, Amir

2013-04-01

Understanding root-soil interactions is of high importance for environmental and agricultural management. Root uptake is an essential component in water and solute transport modeling. The amount of groundwater recharge and solute leaching significantly depends on the demand based plant extraction via its root system. Plant uptake however not only responds to the potential demand, but in most situations is limited by supply form the soil. The ability of the plant to access water and solutes in the soil is governed mainly by root distribution. Particularly under conditions of heterogeneous distribution of water and solutes in the soil, it is essential to capture the interaction between soil and roots. Root architecture models allow studying plant uptake from soil by describing growth and branching of root axes in the soil. Currently root architecture models are able to respond dynamically to water and nutrient distribution in the soil by directed growth (tropism), modified branching and enhanced exudation. The porous soil medium as rooting environment in these models is generally described by classical macroscopic water retention and sorption models, average over the pore scale. In our opinion this simplified description of the root growth medium implies several shortcomings for better understanding root-soil interactions: (i) It is well known that roots grow preferentially in preexisting pores, particularly in more rigid/dry soil. Thus the pore network contributes to the architectural form of the root system; (ii) roots themselves can influence the pore network by creating preferential flow paths (biopores) which are an essential element of structural porosity with strong impact on transport processes; (iii) plant uptake depend on both the spatial location of water/solutes in the pore network as well as the spatial distribution of roots. We therefore consider that for advancing our understanding in root-soil interactions, we need not only to extend our root models

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…

Relationships between root respiration rate and root morphology, chemistry and anatomy in Larix gmelinii and Fraxinus mandshurica.

PubMed

Jia, Shuxia; McLaughlin, Neil B; Gu, Jiacun; Li, Xingpeng; Wang, Zhengquan

2013-06-01

Tree roots are highly heterogeneous in form and function. Previous studies revealed that fine root respiration was related to root morphology, tissue nitrogen (N) concentration and temperature, and varied with both soil depth and season. The underlying mechanisms governing the relationship between root respiration and root morphology, chemistry and anatomy along the root branch order have not been addressed. Here, we examined these relationships of the first- to fifth-order roots for near surface roots (0-10 cm) of 22-year-old larch (Larix gmelinii L.) and ash (Fraxinus mandshurica L.) plantations. Root respiration rate at 18 °C was measured by gas phase O2 electrodes across the first five branching order roots (the distal roots numbered as first order) at three times of the year. Root parameters of root diameter, specific root length (SRL), tissue N concentration, total non-structural carbohydrates (starch and soluble sugar) concentration (TNC), cortical thickness and stele diameter were also measured concurrently. With increasing root order, root diameter, TNC and the ratio of root TNC to tissue N concentration increased, while the SRL, tissue N concentration and cortical proportion decreased. Root respiration rate also monotonically decreased with increasing root order in both species. Cortical tissue (including exodermis, cortical parenchyma and endodermis) was present in the first three order roots, and cross sections of the cortex for the first-order root accounted for 68% (larch) and 86% (ash) of the total cross section of the root. Root respiration was closely related to root traits such as diameter, SRL, tissue N concentration, root TNC : tissue N ratio and stele-to-root diameter proportion among the first five orders, which explained up to 81-94% of variation in the rate of root respiration for larch and up to 83-93% for ash. These results suggest that the systematic variations of root respiration rate within tree fine root system are possibly due to the

Involvement of Arabidopsis thaliana phospholipase Dzeta2 in root hydrotropism through the suppression of root gravitropism.

PubMed

Taniguchi, Yukimi Y; Taniguchi, Masatoshi; Tsuge, Tomohiko; Oka, Atsuhiro; Aoyama, Takashi

2010-01-01

Root hydrotropism is the phenomenon of directional root growth toward moisture under water-deficient conditions. Although physiological and genetic studies have revealed the involvement of the root cap in the sensing of moisture gradients, and those of auxin and abscisic acid (ABA) in the signal transduction for asymmetric root elongation, the overall mechanism of root hydrotropism is still unclear. We found that the promoter activity of the Arabidopsis phospholipase Dzeta2 gene (PLDzeta2) was localized to epidermal cells in the distal root elongation zone and lateral root cap cells adjacent to them, and that exogenous ABA enhanced the activity and extended its area to the entire root cap. Although pldzeta2 mutant root caps did not exhibit a morphological phenotype in either the absence or presence of exogenous ABA, the inhibitory effect of ABA on gravitropism, which was significant in wild-type roots, was not observed in pldzeta2 mutant roots. In root hydrotropism experiments, pldzeta2 mutations significantly retarded or disturbed root hydrotropic responses. A drought condition similar to that used in a hydrotropism experiment enhanced the PLDzeta2 promoter activity in the root cap, as did exogenous ABA. These results suggest that PLDzeta2 responds to drought through ABA signaling in the root cap and accelerates root hydrotropism through the suppression of root gravitropism.

Inhibition of auxin movement from the shoot into the root inhibits lateral root development in Arabidopsis

NASA Technical Reports Server (NTRS)

Reed, R. C.; Brady, S. R.; Muday, G. K.

1998-01-01

In roots two distinct polar movements of auxin have been reported that may control different developmental and growth events. To test the hypothesis that auxin derived from the shoot and transported toward the root controls lateral root development, the two polarities of auxin transport were uncoupled in Arabidopsis. Local application of the auxin-transport inhibitor naphthylphthalamic acid (NPA) at the root-shoot junction decreased the number and density of lateral roots and reduced the free indoleacetic acid (IAA) levels in the root and [3H]IAA transport into the root. Application of NPA to the basal half of or at several positions along the root only reduced lateral root density in regions that were in contact with NPA or in regions apical to the site of application. Lateral root development was restored by application of IAA apical to NPA application. Lateral root development in Arabidopsis roots was also inhibited by excision of the shoot or dark growth and this inhibition was reversible by IAA. Together, these results are consistent with auxin transport from the shoot into the root controlling lateral root development.

A role for the root cap in root branching revealed by the non-auxin probe naxillin.

PubMed

De Rybel, Bert; Audenaert, Dominique; Xuan, Wei; Overvoorde, Paul; Strader, Lucia C; Kepinski, Stefan; Hoye, Rebecca; Brisbois, Ronald; Parizot, Boris; Vanneste, Steffen; Liu, Xing; Gilday, Alison; Graham, Ian A; Nguyen, Long; Jansen, Leentje; Njo, Maria Fransiska; Inzé, Dirk; Bartel, Bonnie; Beeckman, Tom

2012-09-01

The acquisition of water and nutrients by plant roots is a fundamental aspect of agriculture and strongly depends on root architecture. Root branching and expansion of the root system is achieved through the development of lateral roots and is to a large extent controlled by the plant hormone auxin. However, the pleiotropic effects of auxin or auxin-like molecules on root systems complicate the study of lateral root development. Here we describe a small-molecule screen in Arabidopsis thaliana that identified naxillin as what is to our knowledge the first non-auxin-like molecule that promotes root branching. By using naxillin as a chemical tool, we identified a new function for root cap-specific conversion of the auxin precursor indole-3-butyric acid into the active auxin indole-3-acetic acid and uncovered the involvement of the root cap in root branching. Delivery of an auxin precursor in peripheral tissues such as the root cap might represent an important mechanism shaping root architecture.

A role for the root cap in root branching revealed by the non-auxin probe naxillin

PubMed Central

De Rybel, Bert; Audenaert, Dominique; Xuan, Wei; Overvoorde, Paul; Strader, Lucia C; Kepinski, Stefan; Hoye, Rebecca; Brisbois, Ronald; Parizot, Boris; Vanneste, Steffen; Liu, Xing; Gilday, Alison; Graham, Ian A; Nguyen, Long; Jansen, Leentje; Njo, Maria Fransiska; Inzé, Dirk; Bartel, Bonnie; Beeckman, Tom

2013-01-01

The acquisition of water and nutrients by plant roots is a fundamental aspect of agriculture and strongly depends on root architecture. Root branching and expansion of the root system is achieved through the development of lateral roots and is to a large extent controlled by the plant hormone auxin. However, the pleiotropic effects of auxin or auxin-like molecules on root systems complicate the study of lateral root development. Here we describe a small-molecule screen in Arabidopsis thaliana that identified naxillin as what is to our knowledge the first non-auxin-like molecule that promotes root branching. By using naxillin as a chemical tool, we identified a new function for root cap-specific conversion of the auxin precursor indole-3-butyric acid into the active auxin indole-3-acetic acid and uncovered the involvement of the root cap in root branching. Delivery of an auxin precursor in peripheral tissues such as the root cap might represent an important mechanism shaping root architecture. PMID:22885787

Hydrogen sulfide alleviates mercury toxicity by sequestering it in roots or regulating reactive oxygen species productions in rice seedlings.

PubMed

Chen, Zhen; Chen, Moshun; Jiang, Ming

2017-02-01

Soil mercury (Hg) contamination is a major factor that affects agricultural yield and food security. Hydrogen sulfide (H 2 S) plays multifunctional roles in mediating a variety of responses to abiotic stresses. The effects of exogenous H 2 S on rice (Oryza sativa var 'Nipponbare') growth and metabolism under mercuric chloride (HgCl 2 ) stress were investigated in this study. Either 100 or 200 μM sodium hydrosulfide (NaHS, a donor of H 2 S) pretreatment improved the transcription of bZIP60, a membrane-associated transcription factor, and then enhanced the expressions of non-protein thiols (NPT) and metallothioneins (OsMT-1) to sequester Hg in roots and thus inhibit Hg transport to shoots. Meanwhile, H 2 S promoted seedlings growth significantly even in the presences of Hg and superoxide dismutase (SOD, EC 1.15.1.1) or catalase (CAT, EC 1.11.1.6) inhibitors, diethyldithiocarbamate (DDC) or 3-amino-1,2,4-triazole (AT). H 2 S might act as an antioxidant to inhibit or scavenge reactive oxygen species (ROS) productions for maintaining the lower MDA and H 2 O 2 levels, and thereby preventing oxidative damages. All these results indicated H 2 S effectively alleviated Hg toxicity by sequestering it in roots or by regulating ROS in seedlings and then thus significantly promoted rice growth. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Low Light Availability Alters Root Exudation and Reduces Putative Beneficial Microorganisms in Seagrass Roots

PubMed Central

Martin, Belinda C.; Gleeson, Deirdre; Statton, John; Siebers, Andre R.; Grierson, Pauline; Ryan, Megan H.; Kendrick, Gary A.

2018-01-01

Seagrass roots host a diverse microbiome that is critical for plant growth and health. Composition of microbial communities can be regulated in part by root exudates, but the specifics of these interactions in seagrass rhizospheres are still largely unknown. As light availability controls primary productivity, reduced light may impact root exudation and consequently the composition of the root microbiome. Hence, we analyzed the influence of light availability on root exudation and community structure of the root microbiome of three co-occurring seagrass species, Halophila ovalis, Halodule uninervis and Cymodocea serrulata. Plants were grown under four light treatments in mesocosms for 2 weeks; control (100% surface irradiance (SI), medium (40% SI), low (20% SI) and fluctuating light (10 days 20% and 4 days 100%). 16S rDNA amplicon sequencing revealed that microbial diversity, composition and predicted function were strongly influenced by the presence of seagrass roots, such that root microbiomes were unique to each seagrass species. Reduced light availability altered seagrass root exudation, as characterized using fluorescence spectroscopy, and altered the composition of seagrass root microbiomes with a reduction in abundance of potentially beneficial microorganisms. Overall, this study highlights the potential for above-ground light reduction to invoke a cascade of changes from alterations in root exudation to a reduction in putative beneficial microorganisms and, ultimately, confirms the importance of the seagrass root environment – a critical, but often overlooked space. PMID:29375529

Negative gravitropism in plant roots.

PubMed

Ge, Liangfa; Chen, Rujin

2016-10-17

Plants are capable of orienting their root growth towards gravity in a process termed gravitropism, which is necessary for roots to grow into soil, for water and nutrient acquisition and to anchor plants. Here we show that root gravitropism depends on the novel protein, NEGATIVE GRAVITROPIC RESPONSE OF ROOTS (NGR). In both Medicago truncatula and Arabidopsis thaliana, loss of NGR reverses the direction of root gravitropism, resulting in roots growing upward.

Root gravitropism

NASA Technical Reports Server (NTRS)

Masson, P. H.

1995-01-01

When a plant root is reoriented within the gravity field, it responds by initiating a curvature which eventually results in vertical growth. Gravity sensing occurs primarily in the root tip. It may involve amyloplast sedimentation in the columella cells of the root cap, or the detection of forces exerted by the mass of the protoplast on opposite sides of its cell wall. Gravisensing activates a signal transduction cascade which results in the asymmetric redistribution of auxin and apoplastic Ca2+ across the root tip, with accumulation at the bottom side. The resulting lateral asymmetry in Ca2+ and auxin concentration is probably transmitted to the elongation zone where differential cellular elongation occurs until the tip resumes vertical growth. The Cholodny-Went theory proposes that gravity-induced auxin redistribution across a gravistimulated plant organ is responsible for the gravitropic response. However, recent data indicate that the gravity-induced reorientation is more complex, involving both auxin gradient-dependent and auxin gradient-independent events.

Genetic and morphological contrasts between wild and anthropogenic populations of Agave parryi var. huachucensis in south-eastern Arizona.

PubMed

Parker, Kathleen C; Trapnell, Dorset W; Hamrick, J L; Hodgson, Wendy C

2014-05-01

At least seven species of Agave, including A. parryi, were cultivated prehistorically in Arizona, serving as important sources of food and fibre. Many relict populations from ancient cultivation remain in the modern landscape, offering a unique opportunity to study pre-Columbian plant manipulation practices. This study examined genetic and morphological variation in six A. p. var. huachucensis populations of unknown origin to compare them with previous work on A. parryi populations of known origin, to infer their cultivation history and to determine whether artificial selection is evident in populations potentially managed by early agriculturalists. Six A. p. var. huachucensis and 17 A. parryi populations were sampled, and morphometric, allozyme and microsatellite data were used to compare morphology and genetic structure in purportedly anthropogenic and wild populations, as well as in the two taxa. Analysis of molecular variance and Bayesian clustering were performed to partition variation associated with taxonomic identity and hypothesized evolutionary history, to highlight patterns of similarity among populations and to identify potential wild sources for the planting stock. A p. var. huachucensis and A. parryi populations differed significantly both morphologically and genetically. Like A. parryi, wild A. p. var. huachucensis populations were more genetically diverse than the inferred anthropogenic populations, with greater expected heterozygosity, percentage of polymorphic loci and number of alleles. Inferred anthropogenic populations exhibited many traits indicative of past active cultivation: greater morphological uniformity, fixed heterozygosity for several loci (non-existent in wild populations), fewer multilocus genotypes and strong differentiation among populations. Where archaeological information is lacking, the genetic signature of many Agave populations in Arizona can be used to infer their evolutionary history and to identify potentially fruitful

Genetic and morphological contrasts between wild and anthropogenic populations of Agave parryi var. huachucensis in south-eastern Arizona

PubMed Central

Parker, Kathleen C.; Trapnell, Dorset W.; Hamrick, J. L.; Hodgson, Wendy C.

2014-01-01

Background and Aims At least seven species of Agave, including A. parryi, were cultivated prehistorically in Arizona, serving as important sources of food and fibre. Many relict populations from ancient cultivation remain in the modern landscape, offering a unique opportunity to study pre-Columbian plant manipulation practices. This study examined genetic and morphological variation in six A. p. var. huachucensis populations of unknown origin to compare them with previous work on A. parryi populations of known origin, to infer their cultivation history and to determine whether artificial selection is evident in populations potentially managed by early agriculturalists. Methods Six A. p. var. huachucensis and 17 A. parryi populations were sampled, and morphometric, allozyme and microsatellite data were used to compare morphology and genetic structure in purportedly anthropogenic and wild populations, as well as in the two taxa. Analysis of molecular variance and Bayesian clustering were performed to partition variation associated with taxonomic identity and hypothesized evolutionary history, to highlight patterns of similarity among populations and to identify potential wild sources for the planting stock. Key Results A p. var. huachucensis and A. parryi populations differed significantly both morphologically and genetically. Like A. parryi, wild A. p. var. huachucensis populations were more genetically diverse than the inferred anthropogenic populations, with greater expected heterozygosity, percentage of polymorphic loci and number of alleles. Inferred anthropogenic populations exhibited many traits indicative of past active cultivation: greater morphological uniformity, fixed heterozygosity for several loci (non-existent in wild populations), fewer multilocus genotypes and strong differentiation among populations. Conclusions Where archaeological information is lacking, the genetic signature of many Agave populations in Arizona can be used to infer their

LenVarDB: database of length-variant protein domains.

PubMed

Mutt, Eshita; Mathew, Oommen K; Sowdhamini, Ramanathan

2014-01-01

Protein domains are functionally and structurally independent modules, which add to the functional variety of proteins. This array of functional diversity has been enabled by evolutionary changes, such as amino acid substitutions or insertions or deletions, occurring in these protein domains. Length variations (indels) can introduce changes at structural, functional and interaction levels. LenVarDB (freely available at http://caps.ncbs.res.in/lenvardb/) traces these length variations, starting from structure-based sequence alignments in our Protein Alignments organized as Structural Superfamilies (PASS2) database, across 731 structural classification of proteins (SCOP)-based protein domain superfamilies connected to 2 730 625 sequence homologues. Alignment of sequence homologues corresponding to a structural domain is available, starting from a structure-based sequence alignment of the superfamily. Orientation of the length-variant (indel) regions in protein domains can be visualized by mapping them on the structure and on the alignment. Knowledge about location of length variations within protein domains and their visual representation will be useful in predicting changes within structurally or functionally relevant sites, which may ultimately regulate protein function. Non-technical summary: Evolutionary changes bring about natural changes to proteins that may be found in many organisms. Such changes could be reflected as amino acid substitutions or insertions-deletions (indels) in protein sequences. LenVarDB is a database that provides an early overview of observed length variations that were set among 731 protein families and after examining >2 million sequences. Indels are followed up to observe if they are close to the active site such that they can affect the activity of proteins. Inclusion of such information can aid the design of bioengineering experiments.

A new anatomically based nomenclature for the roots and root canals-part 1: maxillary molars.

PubMed

Kottoor, Jojo; Albuquerque, Denzil Valerian; Velmurugan, Natanasabapathy

2012-01-01

Numerous terminologies have been employed in the dental literature to describe the roots and root canal systems of maxillary molars. This multiplicity in naming of roots and canals makes the reader susceptible to misinterpretation and confusion. No consensus thus far has been arrived at for defining the names of roots and root canals in maxillary molars, including their various morphological aberrations. The anatomical relation of roots and their root canals were identified and were subsequently named based on definite sets of criteria. A new method for identification and naming of roots and root canal anatomy in maxillary molars, based on their root and canal relationship, was formulated and is presented in this paper. The nomenclature makes certain essential modifications to the traditional approach to accommodate naming of the various aberrations presented in the maxillary molars. A simple, yet extensive, nomenclature system has been proposed that appropriately names the internal and external morphology of maxillary molars.

Fine root mercury heterogeneity: metabolism of lower-order roots as an effective route for mercury removal.

PubMed

Wang, Jun-Jian; Guo, Ying-Ying; Guo, Da-Li; Yin, Sen-Lu; Kong, De-Liang; Liu, Yang-Sheng; Zeng, Hui

2012-01-17

Fine roots are critical components for plant mercury (Hg) uptake and removal, but the patterns of Hg distribution and turnover within the heterogeneous fine root components and their potential limiting factors are poorly understood. Based on root branching structure, we studied the total Hg (THg) and its cellular partitioning in fine roots in 6 Chinese subtropical trees species and the impacts of root morphological and stoichiometric traits on Hg partitioning. The THg concentration generally decreased with increasing root order, and was higher in cortex than in stele. This concentration significantly correlated with root length, diameter, specific root length, specific root area, and nitrogen concentration, whereas its cytosolic fraction (accounting for <10% of THg) correlated with root carbon and sulfur concentrations. The estimated Hg return flux from dead fine roots outweighed that from leaf litter, and ephemeral first-order roots that constituted 7.2-22.3% of total fine root biomass may have contributed most to this flux (39-71%, depending on tree species and environmental substrate). Our results highlight the high capacity of Hg stabilization and Hg return by lower-order roots and demonstrate that turnover of lower-order roots may be an effective strategy of detoxification in perennial tree species.

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.

[The influence of colonizing methylobacteria on morphogenesis and resistance of sugar beet and white cabbage plants to Erwinia carotovora].

PubMed

Pigoleva, S V; Zakharchenko, N S; Pigolev, A V; Trotsenko, Iu A; Bur'ianov, Ia I

2009-01-01

The influence of colonization of sugar beet (Beta vulgaris var. saccharifera (Alef) Krass) and white cabbage (Brassica oleracea var. capitata L.) plants by methylotrophic bacteria Methylovorus mays on the growth, rooting, and plant resistance to phytopathogen bacteria Erwinia carotovora was investigated. The colonization by methylobacteria led to their steady association with the plants which had increased growth speed, root formation and photosynthetic activity. The colonized plants had increased resistance to Erwinia carotovora phytopathogen and were better adapted to greenhouse conditions. The obtained results showed the perspectives for the practical implementation of methylobacteria in the ecologically clean microbiology substances used as the plant growth stimulators and for the plant protection from pathogens.

Responses of grapevine rootstocks to drought through altered root system architecture and root transcriptomic regulations.

PubMed

Yıldırım, Kubilay; Yağcı, Adem; Sucu, Seda; Tunç, Sümeyye

2018-06-01

Roots are the major interface between the plant and various stress factors in the soil environment. Alteration of root system architecture (RSA) (root length, spread, number and length of lateral roots) in response to environmental changes is known to be an important strategy for plant adaptation and productivity. In light of ongoing climate changes and global warming predictions, the breeding of drought-tolerant grapevine cultivars is becoming a crucial factor for developing a sustainable viticulture. Root-trait modeling of grapevine rootstock for drought stress scenarios, together with high-throughput phenotyping and genotyping techniques, may provide a valuable background for breeding studies in viticulture. Here, tree grafted grapevine rootstocks (110R, 5BB and 41B) having differential RSA regulations and drought tolerance were investigated to define their drought dependent root characteristics. Root area, root length, ramification and number of root tips reduced less in 110R grafted grapevines compared to 5BB and 41B grafted ones during drought treatment. Root relative water content as well as total carbohydrate and nitrogen content were found to be much higher in the roots of 110R than it was in the roots of other rootstocks under drought. Microarray-based root transcriptome profiling was also conducted on the roots of these rootstocks to identify their gene regulation network behind drought-dependent RSA alterations. Transcriptome analysis revealed totally 2795, 1196 and 1612 differentially expressed transcripts at the severe drought for the roots of 110R, 5BB and 41B, respectively. According to this transcriptomic data, effective root elongation and enlargement performance of 110R were suggested to depend on three transcriptomic regulations. First one is the drought-dependent induction in sugar and protein transporters genes (SWEET and NRT1/PTR) in the roots of 110R to facilitate carbohydrate and nitrogen accumulation. In the roots of the same rootstock

Physiological Characterization and Comparative Transcriptome Analysis of White and Green Leaves of Ananas comosus var. bracteatus

PubMed Central

Li, Xia; Kanakala, Surapathrudu; He, Yehua; Zhong, Xiaolan; Yu, Sanmiao; Li, Ruixue; Sun, Lingxia; Ma, Jun

2017-01-01

Leaf coloration is one of the most important and attractive characteristics of Ananas comosus var. bracteatus. The chimeric character is not stable during the in vitro tissue culturing. Many regenerated plants lost economic values for the loss of the chimeric character of leaves. In order to reveal the molecular mechanisms involved in the albino phenotype of the leaf cells, the physiological and transcriptional differences between complete white (CWh) and green (CGr) leaf cells of A. comosus var. bracteatus were analyzed. A total of 1,431 differentially expressed unigenes (DEGs) in CGr and CWh leaves were identified using RNA-seq. A comparison to the COG, GO and KEGG annotations revealed DEGs involved in chlorophyll biosynthesis, chloroplast development and photosynthesis. Furthermore, the measurement of main precursors of chlorophyll in the CWh leaves confirmed that the rate-limiting step in chlorophyll biosynthesis, and thus the cause of the albino phenotype of the white cells, was the conversion of pyrrole porphobilinogen (PBG) to uroporphyrinogen III (Uro III). The enzyme activity of porphobilinogen deaminase (PBGD) and uroporporphyrinogn III synthase (UROS), which catalyze the transition of PBG to Uro III, was significantly decreased in the CWh leaves. Our data showed the transcriptional differences between the CWh and CGr plants and characterized key steps in chlorophyll biosynthesis of the CWh leaves. These results contribute to our understanding of the mechanisms and regulation of pigment biosynthesis in the CWh leaf cells of A. comosus var. bracteatus. PMID:28095462

Physiological Characterization and Comparative Transcriptome Analysis of White and Green Leaves of Ananas comosus var. bracteatus.

PubMed

Li, Xia; Kanakala, Surapathrudu; He, Yehua; Zhong, Xiaolan; Yu, Sanmiao; Li, Ruixue; Sun, Lingxia; Ma, Jun

2017-01-01

Leaf coloration is one of the most important and attractive characteristics of Ananas comosus var. bracteatus. The chimeric character is not stable during the in vitro tissue culturing. Many regenerated plants lost economic values for the loss of the chimeric character of leaves. In order to reveal the molecular mechanisms involved in the albino phenotype of the leaf cells, the physiological and transcriptional differences between complete white (CWh) and green (CGr) leaf cells of A. comosus var. bracteatus were analyzed. A total of 1,431 differentially expressed unigenes (DEGs) in CGr and CWh leaves were identified using RNA-seq. A comparison to the COG, GO and KEGG annotations revealed DEGs involved in chlorophyll biosynthesis, chloroplast development and photosynthesis. Furthermore, the measurement of main precursors of chlorophyll in the CWh leaves confirmed that the rate-limiting step in chlorophyll biosynthesis, and thus the cause of the albino phenotype of the white cells, was the conversion of pyrrole porphobilinogen (PBG) to uroporphyrinogen III (Uro III). The enzyme activity of porphobilinogen deaminase (PBGD) and uroporporphyrinogn III synthase (UROS), which catalyze the transition of PBG to Uro III, was significantly decreased in the CWh leaves. Our data showed the transcriptional differences between the CWh and CGr plants and characterized key steps in chlorophyll biosynthesis of the CWh leaves. These results contribute to our understanding of the mechanisms and regulation of pigment biosynthesis in the CWh leaf cells of A. comosus var. bracteatus.

Phytoremediation of petroleum-polluted soils: application of Polygonum aviculare and its root-associated (penetrated) fungal strains for bioremediation of petroleum-polluted soils.

PubMed

Mohsenzadeh, Fariba; Nasseri, Simin; Mesdaghinia, Alireza; Nabizadeh, Ramin; Zafari, Doustmorad; Khodakaramian, Gholam; Chehregani, Abdolkarim

2010-05-01

Petroleum-polluted soils are a common disaster in many countries. Bioremediation of oil contamination in soils is based on the stimulation of petroleum-hydrocarbon-degrading fungal and microbial communities. A field study was conducted in a petroleum-contaminated site to find petroleum-resistant plants and their root-associated fungal strains for use in bioremediation of petroleum-polluted soils. Results and observations showed that the amounts of petroleum pollution in nonvegetated soils were several times higher than in vegetated soils. Plants collected from petroleum-polluted areas were identified using morphological characters. Results indicated that seven plant species were growing on the contaminated sites: Alhaji cameleron L. (Fabaceae), Amaranthus retroflexus L. var. retroflexus (Amaranthaceae), Convolvulus arvensis L. (Convolvulaceae), Chrozophora hierosolymitana Spreg. (Euphorbiaceae), Noea mucronata L. (Boraginaceae), Poa sp. (Poaceae), and Polygonum aviculare L. (Polygonaceae). The root-associated fungi of each plant were determined and results showed the presence of 11 species that associated with and also penetrated the roots of plants growing in the polluted areas. Altenaria sp. was common to all of the plants and the others had species-specific distribution within the plants. The largest numbers of fungal species (six) were determined for P. aviculare and Poa sp. in polluted areas. However, the variation of fungal strains in the plants collected from petroleum-polluted areas was greater than for nonpolluted ones. Culture of fungi in oil-contaminated media showed that all the studied fungi were resistant to low petroleum pollution (1% v/v) and a few species, especially Fusarium species, showed resistance to higher petroleum pollution (10% v/v) and may be suitable for bioremediation in highly polluted areas. Bioremediation tests with P. aviculare, with and without fungal strains, showed that application of both the plant and its root-associated fungal

Complete plastid genome of Astragalus mongholicus var. nakaianus (Fabaceae).

PubMed

Choi, In-Su; Kim, Joo-Hwan; Choi, Byoung-Hee

2016-07-01

The first complete plastid genome (plastome) of the largest angiosperm genus, Astragalus, was sequenced for the Korean endangered endemic species A. mongholicus var. nakaianus. Its genome is relatively short (123,633 bp) because it lacks an Inverted Repeat (IR) region. It comprises 110 genes, including four unique rRNAs, 30 tRNAs, and 76 protein-coding genes. Similar to other closely related plastomes, rpl22 and rps16 are absent. The putative pseudogene with abnormal stop codons is atpE. This plastome has no additional inversions when compared with highly variable plastomes from IRLC tribes Fabeae and Trifolieae. Our phylogenetic analysis confirms the non-monophyly of Galegeae.

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).

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

In vitro screening of probiotic properties of Saccharomyces cerevisiae var. boulardii and food-borne Saccharomyces cerevisiae strains.

PubMed

van der Aa Kühle, Alis; Skovgaard, Kerstin; Jespersen, Lene

2005-05-01

The probiotic potential of 18 Saccharomyces cerevisiae strains used for production of foods or beverages or isolated from such, and eight strains of Saccharomyces cerevisiae var. boulardii, was investigated. All strains included were able to withstand pH 2.5 and 0.3% Oxgall. Adhesion to the nontumorigenic porcine jejunal epithelial cell line (IPEC-J2) was investigated by incorporation of 3H-methionine into the yeast cells and use of liquid scintillation counting. Only few of the food-borne S. cerevisiae strains exhibited noteworthy adhesiveness with the strongest levels of adhesion (13.6-16.8%) recorded for two isolates from blue veined cheeses. Merely 25% of the S. cerevisiae var. boulardii strains displayed good adhesive properties (16.2-28.0%). The expression of the proinflammatory cytokine IL-1alpha decreased strikingly in IPEC-J2 cells exposed to a Shiga-like toxin 2e producing Escherichia coli strain when the cells were pre- and coincubated with S. cerevisiae var. boulardii even though this yeast strain was low adhesive (5.4%), suggesting that adhesion is not a mandatory prerequisite for such a probiotic effect. A strain of S. cerevisiae isolated from West African sorghum beer exerted similar effects hence indicating that food-borne strains of S. cerevisiae may possess probiotic properties in spite of low adhesiveness.

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

Contrasting responses of root morphology and root-exuded organic acids to low phosphorus availability in three important food crops with divergent root traits.

PubMed

Wang, Yan-Liang; Almvik, Marit; Clarke, Nicholas; Eich-Greatorex, Susanne; Øgaard, Anne Falk; Krogstad, Tore; Lambers, Hans; Clarke, Jihong Liu

2015-08-17

Phosphorus (P) is an important element for crop productivity and is widely applied in fertilizers. Most P fertilizers applied to land are sorbed onto soil particles, so research on improving plant uptake of less easily available P is important. In the current study, we investigated the responses in root morphology and root-exuded organic acids (OAs) to low available P (1 μM P) and sufficient P (50 μM P) in barley, canola and micropropagated seedlings of potato-three important food crops with divergent root traits, using a hydroponic plant growth system. We hypothesized that the dicots canola and tuber-producing potato and the monocot barley would respond differently under various P availabilities. WinRHIZO and liquid chromatography triple quadrupole mass spectrometry results suggested that under low P availability, canola developed longer roots and exhibited the fastest root exudation rate for citric acid. Barley showed a reduction in root length and root surface area and an increase in root-exuded malic acid under low-P conditions. Potato exuded relatively small amounts of OAs under low P, while there was a marked increase in root tips. Based on the results, we conclude that different crops show divergent morphological and physiological responses to low P availability, having evolved specific traits of root morphology and root exudation that enhance their P-uptake capacity under low-P conditions. These results could underpin future efforts to improve P uptake of the three crops that are of importance for future sustainable crop production. Published by Oxford University Press on behalf of the Annals of Botany Company.

[Fitness of sexual reproduction of Toona ciliata var. pubescens natural populations and their sexual reproduction and regeneration].

PubMed

Huang, Hong Lan; Zhang, Lu; Jia, Li Ming; Liang, Yue-Long; Cai, Jun Huo