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Sample records for putative alfalfa helicase

  1. ALFALFA

    OpenAIRE

    Mirko Stjepanović; Robert Zimmer; Marijana Tucak; Gordana Bukvić; Svetislav Popović; Zvonimir Štafa

    2009-01-01

    The academic textbook Alfalfa contains the following chapters: Review outline, Foreword, Origin and spread of alfalfa, Economic importance of alfalfa, Biological properties and breeding alfalfa, Morphological traits of alfalfa, Growth and development of alfalfa, Ecological conditions for alfalfa growth, Agronomy of alfalfa for fodder production, Pests and diseases of alfalfa and their control, Usage of alfalfa and hay, silage and haylage production, Alfalfa seed production, Prospects for alfa...

  2. ALFALFA

    Directory of Open Access Journals (Sweden)

    Mirko Stjepanović

    2009-12-01

    Full Text Available The academic textbook Alfalfa contains the following chapters: Review outline, Foreword, Origin and spread of alfalfa, Economic importance of alfalfa, Biological properties and breeding alfalfa, Morphological traits of alfalfa, Growth and development of alfalfa, Ecological conditions for alfalfa growth, Agronomy of alfalfa for fodder production, Pests and diseases of alfalfa and their control, Usage of alfalfa and hay, silage and haylage production, Alfalfa seed production, Prospects for alfalfa in Croatia, Index and interpreter of terms and abbreviations, About authors. How to satisfy requirements of the “queen of fodder crops“ to achieve high yields of high quality fodder is the issue presented in the book Alfalfa is being grown in Croatia on about 42 000 hectares. Average fodder yields are low, about 5 t ha1, so the employment of genetical potential of varieties in rainfed farming is 35 to 40%, making the production more expensive.

  3. Alfalfa

    Science.gov (United States)

    Alfalfa is an herb. People use the leaves, sprouts, and seeds to make medicine. Alfalfa is used for kidney conditions, bladder and prostate ... bleeding disorder called thrombocytopenic purpura. People also take alfalfa as a source of vitamins A, C, E, ...

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

    Science.gov (United States)

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

    2014-01-01

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

  5. SAD-3, a Putative Helicase Required for Meiotic Silencing by Unpaired DNA, Interacts with Other Components of the Silencing Machinery

    Science.gov (United States)

    Hammond, Thomas M.; Xiao, Hua; Boone, Erin C.; Perdue, Tony D.; Pukkila, Patricia J.; Shiu, Patrick K. T.

    2011-01-01

    In Neurospora crassa, genes lacking a pairing partner during meiosis are suppressed by a process known as meiotic silencing by unpaired DNA (MSUD). To identify novel MSUD components, we have developed a high-throughput reverse-genetic screen for use with the N. crassa knockout library. Here we describe the screening method and the characterization of a gene (sad-3) subsequently discovered. SAD-3 is a putative helicase required for MSUD and sexual spore production. It exists in a complex with other known MSUD proteins in the perinuclear region, a center for meiotic silencing activity. Orthologs of SAD-3 include Schizosaccharomyces pombe Hrr1, a helicase required for RNAi-induced heterochromatin formation. Both SAD-3 and Hrr1 interact with an RNA-directed RNA polymerase and an Argonaute, suggesting that certain aspects of silencing complex formation may be conserved between the two fungal species. PMID:22384347

  6. A temperature-sensitive allele of a putative mRNA splicing helicase down-regulates many cell wall genes and causes radial swelling in Arabidopsis thaliana.

    Science.gov (United States)

    Howles, Paul A; Gebbie, Leigh K; Collings, David A; Varsani, Arvind; Broad, Ronan C; Ohms, Stephen; Birch, Rosemary J; Cork, Ann H; Arioli, Tony; Williamson, Richard E

    2016-05-01

    The putative RNA helicase encoded by the Arabidopsis gene At1g32490 is a homolog of the yeast splicing RNA helicases Prp2 and Prp22. We isolated a temperature-sensitive allele (rsw12) of the gene in a screen for root radial swelling mutants. Plants containing this allele grown at the restrictive temperature showed weak radial swelling, were stunted with reduced root elongation, and contained reduced levels of cellulose. The role of the protein was further explored by microarray analysis. By using both fold change cutoffs and a weighted gene coexpression network analysis (WGCNA) to investigate coexpression of genes, we found that the radial swelling phenotype was not linked to genes usually associated with primary cell wall biosynthesis. Instead, the mutation has strong effects on expression of secondary cell wall related genes. Many genes potentially associated with secondary walls were present in the most significant WGCNA module, as were genes coding for arabinogalactans and proteins with GPI anchors. The proportion of up-regulated genes that possess introns in rsw12 was above that expected if splicing was unrelated to the activity of the RNA helicase, suggesting that the helicase does indeed play a role in splicing in Arabidopsis. The phenotype may be due to a change in the expression of one or more genes coding for cell wall proteins.

  7. Structure of the SPRY domain of the human RNA helicase DDX1, a putative interaction platform within a DEAD-box protein

    Energy Technology Data Exchange (ETDEWEB)

    Kellner, Julian N.; Meinhart, Anton, E-mail: anton.meinhart@mpimf-heidelberg.mpg.de [Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg (Germany)

    2015-08-25

    The structure of the SPRY domain of the human RNA helicase DDX1 was determined at 2.0 Å resolution. The SPRY domain provides a putative protein–protein interaction platform within DDX1 that differs from other SPRY domains in its structure and conserved regions. The human RNA helicase DDX1 in the DEAD-box family plays an important role in RNA processing and has been associated with HIV-1 replication and tumour progression. Whereas previously described DEAD-box proteins have a structurally conserved core, DDX1 shows a unique structural feature: a large SPRY-domain insertion in its RecA-like consensus fold. SPRY domains are known to function as protein–protein interaction platforms. Here, the crystal structure of the SPRY domain of human DDX1 (hDSPRY) is reported at 2.0 Å resolution. The structure reveals two layers of concave, antiparallel β-sheets that stack onto each other and a third β-sheet beneath the β-sandwich. A comparison with SPRY-domain structures from other eukaryotic proteins showed that the general β-sandwich fold is conserved; however, differences were detected in the loop regions, which were identified in other SPRY domains to be essential for interaction with cognate partners. In contrast, in hDSPRY these loop regions are not strictly conserved across species. Interestingly, though, a conserved patch of positive surface charge is found that may replace the connecting loops as a protein–protein interaction surface. The data presented here comprise the first structural information on DDX1 and provide insights into the unique domain architecture of this DEAD-box protein. By providing the structure of a putative interaction domain of DDX1, this work will serve as a basis for further studies of the interaction network within the hetero-oligomeric complexes of DDX1 and of its recruitment to the HIV-1 Rev protein as a viral replication factor.

  8. Mutations in the putative zinc-binding motif of UL52 demonstrate a complex interdependence between the UL5 and UL52 subunits of the human herpes simplex virus type 1 helicase/primase complex.

    Science.gov (United States)

    Chen, Yan; Carrington-Lawrence, Stacy D; Bai, Ping; Weller, Sandra K

    2005-07-01

    Herpes simplex virus type 1 (HSV-1) encodes a heterotrimeric helicase-primase (UL5/8/52) complex. UL5 contains seven motifs found in helicase superfamily 1, and UL52 contains conserved motifs found in primases. The contributions of each subunit to the biochemical activities of the complex, however, remain unclear. We have previously demonstrated that a mutation in the putative zinc finger at UL52 C terminus abrogates not only primase but also ATPase, helicase, and DNA-binding activities of a UL5/UL52 subcomplex, indicating a complex interdependence between the two subunits. To test this hypothesis and to further investigate the role of the zinc finger in the enzymatic activities of the helicase-primase, a series of mutations were constructed in this motif. They differed in their ability to complement a UL52 null virus: totally defective, partial complementation, and potentiating. In this study, four of these mutants were studied biochemically after expression and purification from insect cells infected with recombinant baculoviruses. All mutants show greatly reduced primase activity. Complementation-defective mutants exhibited severe defects in ATPase, helicase, and DNA-binding activities. Partially complementing mutants displayed intermediate levels of these activities, except that one showed a wild-type level of helicase activity. These data suggest that the UL52 zinc finger motif plays an important role in the activities of the helicase-primase complex. The observation that mutations in UL52 affected helicase, ATPase, and DNA-binding activities indicates that UL52 binding to DNA via the zinc finger may be necessary for loading UL5. Alternatively, UL5 and UL52 may share a DNA-binding interface.

  9. RecQ Helicases

    DEFF Research Database (Denmark)

    Larsen, Nicolai Balle; Hickson, Ian D

    2013-01-01

    The RecQ family of DNA helicases is highly conserved throughout -evolution, and is important for the maintenance of genome stability. In humans, five RecQ family members have been identified: BLM, WRN, RECQ4, RECQ1 and RECQ5. Defects in three of these give rise to Bloom's syndrome (BLM), Werner...

  10. Genome-Wide Analysis of the RNA Helicase Gene Family in Gossypium raimondii

    Directory of Open Access Journals (Sweden)

    Jie Chen

    2014-03-01

    Full Text Available The RNA helicases, which help to unwind stable RNA duplexes, and have important roles in RNA metabolism, belong to a class of motor proteins that play important roles in plant development and responses to stress. Although this family of genes has been the subject of systematic investigation in Arabidopsis, rice, and tomato, it has not yet been characterized in cotton. In this study, we identified 161 putative RNA helicase genes in the genome of the diploid cotton species Gossypium raimondii. We classified these genes into three subfamilies, based on the presence of either a DEAD-box (51 genes, DEAH-box (52 genes, or DExD/H-box (58 genes in their coding regions. Chromosome location analysis showed that the genes that encode RNA helicases are distributed across all 13 chromosomes of G. raimondii. Syntenic analysis revealed that 62 of the 161 G. raimondii helicase genes (38.5% are within the identified syntenic blocks. Sixty-six (40.99% helicase genes from G. raimondii have one or several putative orthologs in tomato. Additionally, GrDEADs have more conserved gene structures and more simple domains than GrDEAHs and GrDExD/Hs. Transcriptome sequencing data demonstrated that many of these helicases, especially GrDEADs, are highly expressed at the fiber initiation stage and in mature leaves. To our knowledge, this is the first report of a genome-wide analysis of the RNA helicase gene family in cotton.

  11. Alfalfa mosaic virus replicase proteins P1 and P2 interact and colocalize at the vacuolar membrane

    NARCIS (Netherlands)

    Heijden, van der M.W.; Carette, J.E.; Reinhoud, P.J.; Haegi, A.; Bol, J.F.

    2001-01-01

    Replication of Alfalfa mosaic virus (AMV) RNAs depends on the virus-encoded proteins P1 and P2. P1 contains methyltransferase- and helicase-like domains, and P2 contains a polymerase-like domain. Coimmunoprecipitation experiments revealed an interaction between in vitro translated-P1 and P2 and

  12. Reduced Lignin Alfalfa - Update

    Science.gov (United States)

    U.S. farmers harvested alfalfa (Medicago sativa) for hay or haylage from 24.5million acres in 2009. Midwestern states harvested 57 % of 2009 acreage for hay and haylage. However, acreage is stable to declining. Alfalfa provides an excellent source of fiber, protein, minerals and vitamins that partia...

  13. Alfalfa (Medicago sativa L.).

    Science.gov (United States)

    Fu, Chunxiang; Hernandez, Timothy; Zhou, Chuanen; Wang, Zeng-Yu

    2015-01-01

    Alfalfa (Medicago sativa L.) is a high-quality forage crop widely grown throughout the world. This chapter describes an efficient protocol that allows for the generation of large number of transgenic alfalfa plants by sonication-assisted Agrobacterium-mediated transformation. Binary vectors carrying different selectable marker genes that confer resistance to phosphinothricin (bar), kanamycin (npt II), or hygromycin (hph) were used to generate transgenic alfalfa plants. Intact trifoliates collected from clonally propagated plants in the greenhouse were sterilized with bleach and then inoculated with Agrobacterium strain EHA105. More than 80 % of infected leaf pieces could produce rooted transgenic plants in 4-5 months after Agrobacterium-mediated transformation.

  14. Mitochondrial helicases and mitochondrial genome maintenance

    DEFF Research Database (Denmark)

    de Souza-Pinto, Nadja C; Aamann, Maria Diget; Kulikowicz, Tomasz

    2010-01-01

    Helicases are essential enzymes that utilize the energy of nucleotide hydrolysis to drive unwinding of nucleic acid duplexes. Helicases play roles in all aspects of DNA metabolism including DNA repair, DNA replication and transcription. The subcellular locations and functions of several helicases...

  15. Betaines of Alfalfa 1

    Science.gov (United States)

    Wood, Karl V.; Stringham, Kelly J.; Smith, David L.; Volenec, Jeffrey J.; Hendershot, Kerry L.; Jackson, Kimberly A.; Rich, Patrick J.; Yang, Wen-Ju; Rhodes, David

    1991-01-01

    Leaf tissue of alfalfa (Medicago sativa L.) was found to contain prolinebetaine, pipecolatebetaine, hydroxyprolinebetaine, and glycinebetaine. As n-butyl esters, these chemical species exhibit molecular cations at mass/charge ratio (m/z) 200, 214, 216, and 174, respectively, when analyzed by fast atom bombardment mass spectrometry. The underivatized betaines exhibit protonated molecular ions at m/z 144, 158, 160, and 118, respectively, when analyzed by desorption chemical ionization mass spectrometry. Extensive (>45-fold) genotypic variation for hydroxyprolinebetaine level was identified in alfalfa. Because a significant inverse correlation between prolinebetaine and hydroxyprolinebetaine levels was observed among 15 alfalfa genotypes evaluated, it is possible that these compounds may be derived from a common intermediate. Birdsfoot trefoil (Lotus corniculatus L.) contained prolinebetaine, but only traces of glycinebetaine, pipecolatebetaine, and hydroxyprolinebetaine. Red clover (Trifolium pratense L.) lacked prolinebetaine, pipecolatebetaine, and hydroxyprolinebetaine, but contained appreciable levels of both glycinebetaine and trigonelline. Trigonelline was not detectable in the leaf tissue of any alfalfa genotype or cultivar evaluated. PMID:16668271

  16. NUTRITIONAL ENHANCEMENT OF ALFALFA THROUGH GENETIC ENGINEERING

    Directory of Open Access Journals (Sweden)

    J. Faragó

    2008-09-01

    Full Text Available Alfalfa (Medicago sativa L. is a pasture legume crop of primary importance to animal production throughout the world. The nutritional quality of alfalfa, as of other leguminous forage crops, is mainly determined by their content in selected essential amino acids (EAAs, such as methionine (Met and cysteine (Cys. In alfalfa, however, these S-containing amino acids constitute only about 1% or less of crude proteins (Frame et al., 1998. This is significantly less than the 3.5% Met+Cys content in the recommended FAO reference protein (FAO, 1973. Recent advances in genetic engineering allow to use the transgenic approach to increase the content of specific essential amino acids in target plant species. A number of different molecular approaches have been developed to address this issue, such as over-expression of a heterologous or homologous Met-rich protein, expression of a synthetic protein, modification of protein sequence, and metabolic engineering of the free amino acid pool and protein sink. To study the possibility of transgenic enhancement of nutritional quality of alfalfa, we used the approach of expression of a heterologous protein rich in Met+Cys in cells of alfalfa. The T-DNA introduced into the genome of alfalfa, using Agrobacterium tumefaciens-mediated genetic transformation, contained the selectable merker gene nptII for kanamycin (Kn resistance, and a cDNA of Ov gene from Japanese quail (Coturnix coturnix coding for a high Met+Cys containing ovalbumine (Mucha et al., 1991, both under constitutive promoters. After cocultivation of petiole segment- and leaf blade-explants of two highly embryogenic alfalfa genotypes Rg9/I-14-22 and Rg11/I-10-68 (Faragó et al., 1997 with cells of A. tumefaciens strain AGL1 carrying the nptII and Ov genes, and selection of transgenic cells on Kn containing selective media, more than one hundred putatively transgenic regenerants were obtained through somatic embryogenesis. Biological (Kn rooting assay

  17. Genome-wide comparative in silico analysis of the RNA helicase gene family in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza sativa.

    Science.gov (United States)

    Xu, Ruirui; Zhang, Shizhong; Huang, Jinguang; Zheng, Chengchao

    2013-01-01

    RNA helicases are enzymes that are thought to unwind double-stranded RNA molecules in an energy-dependent fashion through the hydrolysis of NTP. RNA helicases are associated with all processes involving RNA molecules, including nuclear transcription, editing, splicing, ribosome biogenesis, RNA export, and organelle gene expression. The involvement of RNA helicase in response to stress and in plant growth and development has been reported previously. While their importance in Arabidopsis and Oryza sativa has been partially studied, the function of RNA helicase proteins is poorly understood in Zea mays and Glycine max. In this study, we identified a total of RNA helicase genes in Arabidopsis and other crop species genome by genome-wide comparative in silico analysis. We classified the RNA helicase genes into three subfamilies according to the structural features of the motif II region, such as DEAD-box, DEAH-box and DExD/H-box, and different species showed different patterns of alternative splicing. Secondly, chromosome location analysis showed that the RNA helicase protein genes were distributed across all chromosomes with different densities in the four species. Thirdly, phylogenetic tree analyses identified the relevant homologs of DEAD-box, DEAH-box and DExD/H-box RNA helicase proteins in each of the four species. Fourthly, microarray expression data showed that many of these predicted RNA helicase genes were expressed in different developmental stages and different tissues under normal growth conditions. Finally, real-time quantitative PCR analysis showed that the expression levels of 10 genes in Arabidopsis and 13 genes in Zea mays were in close agreement with the microarray expression data. To our knowledge, this is the first report of a comparative genome-wide analysis of the RNA helicase gene family in Arabidopsis, Oryza sativa, Zea mays and Glycine max. This study provides valuable information for understanding the classification and putative functions of

  18. Effects of two alfalfa preparations with different particle sizes on the gastric mucosa in weanlings: alfalfa chaff versus alfalfa pellets

    OpenAIRE

    Vondran, Sarah; Venner, Monica; Vervuert, Ingrid

    2016-01-01

    Background Feeding alfalfa hay is often recommended for its buffering components, like protein and calcium, to prevent lesions of the gastric mucosa in horses. Until now, there has been no information regarding the influence of alfalfa particle size on the gastric mucosa. The aim of this study was to investigate the effects of feeding two alfalfa preparations with different particle sizes (alfalfa chaff vs alfalfa pellets) in comparison with grass hay on the gastric mucosa in weanling horses....

  19. Authentic interdomain communication in an RNA helicase reconstituted by expressed protein ligation of two helicase domains.

    Science.gov (United States)

    Karow, Anne R; Theissen, Bettina; Klostermeier, Dagmar

    2007-01-01

    RNA helicases mediate structural rearrangements of RNA or RNA-protein complexes at the expense of ATP hydrolysis. Members of the DEAD box helicase family consist of two flexibly connected helicase domains. They share nine conserved sequence motifs that are involved in nucleotide binding and hydrolysis, RNA binding, and helicase activity. Most of these motifs line the cleft between the two helicase domains, and extensive communication between them is required for RNA unwinding. The two helicase domains of the Bacillus subtilis RNA helicase YxiN were produced separately as intein fusions, and a functional RNA helicase was generated by expressed protein ligation. The ligated helicase binds adenine nucleotides with very similar affinities to the wild-type protein. Importantly, its intrinsically low ATPase activity is stimulated by RNA, and the Michaelis-Menten parameters are similar to those of the wild-type. Finally, ligated YxiN unwinds a minimal RNA substrate to an extent comparable to that of the wild-type helicase, confirming authentic interdomain communication.

  20. Spotted alfalfa aphid, Therioaphis trifolii (Monell) (Hemiptera: Aphididae): Pest on alfalfa in Serbia

    OpenAIRE

    Jovičić, Ivana; Radonjić, Anđa; Petrović-Obradović, Olivera

    2017-01-01

    Spotted alfalfa aphid Therioaphis trifolii (Monell) (Hemiptera, Aphididae) is one of the most important alfalfa pest on the world. Also, it is the most abundant alfalfa aphid in Serbia. This aphid cause damage to alfalfa directly by feeding and indirectly by vectoring plant-pathogenic viruses. Some notes of morphology, host plants, damage, biology, vector role and distribution of spotted alfalfa aphid are given. Abundance of this aphid on alfalfa, influence of climates changes on its abundanc...

  1. Replication of an incomplete alfalfa mosaic virus genome in plants transformed with viral replicase genes

    NARCIS (Netherlands)

    Taschner, P. E.; van der Kuyl, A. C.; Neeleman, L.; Bol, J. F.

    1991-01-01

    RNAs 1 and 2 of alfalfa mosaic virus (AIMV) encode proteins P1 and P2, respectively, both of which have a putative role in viral RNA replication. Tobacco plants were transformed with DNA copies of RNA1 (P1-plants), RNA2 (P2-plants) or a combination of these two cDNAs (P12-plants). All transgenic

  2. MOV10 RNA helicase is a potent inhibitor of retrotransposition in cells.

    Directory of Open Access Journals (Sweden)

    John L Goodier

    Full Text Available MOV10 protein, a putative RNA helicase and component of the RNA-induced silencing complex (RISC, inhibits retrovirus replication. We show that MOV10 also severely restricts human LINE1 (L1, Alu, and SVA retrotransposons. MOV10 associates with the L1 ribonucleoprotein particle, along with other RNA helicases including DDX5, DHX9, DDX17, DDX21, and DDX39A. However, unlike MOV10, these other helicases do not strongly inhibit retrotransposition, an activity dependent upon intact helicase domains. MOV10 association with retrotransposons is further supported by its colocalization with L1 ORF1 protein in stress granules, by cytoplasmic structures associated with RNA silencing, and by the ability of MOV10 to reduce endogenous and ectopic L1 expression. The majority of the human genome is repetitive DNA, most of which is the detritus of millions of years of accumulated retrotransposition. Retrotransposons remain active mutagens, and their insertion can disrupt gene function. Therefore, the host has evolved defense mechanisms to protect against retrotransposition, an arsenal we are only beginning to understand. With homologs in other vertebrates, insects, and plants, MOV10 may represent an ancient and innate form of immunity against both infective viruses and endogenous retroelements.

  3. Purification and crystallization of Kokobera virus helicase

    International Nuclear Information System (INIS)

    De Colibus, Luigi; Speroni, Silvia; Coutard, Bruno; Forrester, Naomi L.; Gould, Ernest; Canard, Bruno; Mattevi, Andrea

    2007-01-01

    Kokobera virus is a mosquito-borne flavivirus belonging, like West Nile virus, to the Japanese encephalitis virus serocomplex. Crystals of the Kokobera virus helicase domain were obtained by the hanging-drop vapour-diffusion method and exhibit a diffraction limit of 2.3 Å. Kokobera virus is a mosquito-borne flavivirus belonging, like West Nile virus, to the Japanese encephalitis virus serocomplex. The flavivirus genus is characterized by a positive-sense single-stranded RNA genome. The unique open reading frame of the viral RNA is transcribed and translated as a single polyprotein which is post-translationally cleaved to yield three structural and seven nonstructural proteins, one of which is the NS3 gene that encodes a C-terminal helicase domain consisting of 431 amino acids. Helicase inhibitors are potential antiviral drugs as the helicase is essential to viral replication. Crystals of the Kokobera virus helicase domain were obtained by the hanging-drop vapour-diffusion method. The crystals belong to space group P3 1 21 (or P3 2 21), with unit-cell parameters a = 88.6, c = 138.6 Å, and exhibit a diffraction limit of 2.3 Å

  4. Helicase-dependent amplification of nucleic acids.

    Science.gov (United States)

    Cao, Yun; Kim, Hyun-Jin; Li, Ying; Kong, Huimin; Lemieux, Bertrand

    2013-10-11

    Helicase-dependent amplification (HDA) is a novel method for the isothermal in vitro amplification of nucleic acids. The HDA reaction selectively amplifies a target sequence by extension of two oligonucleotide primers. Unlike the polymerase chain reaction (PCR), HDA uses a helicase enzyme to separate the deoxyribonucleic acid (DNA) strands, rather than heat denaturation. This allows DNA amplification without the need for thermal cycling. The helicase used in HDA is a helicase super family II protein obtained from a thermophilic organism, Thermoanaerobacter tengcongensis (TteUvrD). This thermostable helicase is capable of unwinding blunt-end nucleic acid substrates at elevated temperatures (60° to 65°C). The HDA reaction can also be coupled with reverse transcription for ribonucleic acid (RNA) amplification. The products of this reaction can be detected during the reaction using fluorescent probes when incubations are conducted in a fluorimeter. Alternatively, products can be detected after amplification using a disposable amplicon containment device that contains an embedded lateral flow strip. Copyright © 2013 John Wiley & Sons, Inc.

  5. Purification and crystallization of Kokobera virus helicase

    Energy Technology Data Exchange (ETDEWEB)

    De Colibus, Luigi; Speroni, Silvia [Department of Genetics and Microbiology, University of Pavia, Via Ferrata 1, 27100 Pavia (Italy); Coutard, Bruno [Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS et Université Aix-Marseille I et II, ESIL, Campus de Luminy, 13288 Marseille CEDEX 09 (France); Forrester, Naomi L.; Gould, Ernest [Centre for Ecology and Hydrology (formerly Institute of Virology), Mansfield Road, Oxford OX1 3SR (United Kingdom); Canard, Bruno [Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS et Université Aix-Marseille I et II, ESIL, Campus de Luminy, 13288 Marseille CEDEX 09 (France); Mattevi, Andrea, E-mail: mattevi@ipvgen.unipv.it [Department of Genetics and Microbiology, University of Pavia, Via Ferrata 1, 27100 Pavia (Italy)

    2007-03-01

    Kokobera virus is a mosquito-borne flavivirus belonging, like West Nile virus, to the Japanese encephalitis virus serocomplex. Crystals of the Kokobera virus helicase domain were obtained by the hanging-drop vapour-diffusion method and exhibit a diffraction limit of 2.3 Å. Kokobera virus is a mosquito-borne flavivirus belonging, like West Nile virus, to the Japanese encephalitis virus serocomplex. The flavivirus genus is characterized by a positive-sense single-stranded RNA genome. The unique open reading frame of the viral RNA is transcribed and translated as a single polyprotein which is post-translationally cleaved to yield three structural and seven nonstructural proteins, one of which is the NS3 gene that encodes a C-terminal helicase domain consisting of 431 amino acids. Helicase inhibitors are potential antiviral drugs as the helicase is essential to viral replication. Crystals of the Kokobera virus helicase domain were obtained by the hanging-drop vapour-diffusion method. The crystals belong to space group P3{sub 1}21 (or P3{sub 2}21), with unit-cell parameters a = 88.6, c = 138.6 Å, and exhibit a diffraction limit of 2.3 Å.

  6. Mutational analysis of an archaeal minichromosome maintenance protein exterior hairpin reveals critical residues for helicase activity and DNA binding

    Directory of Open Access Journals (Sweden)

    Brewster Aaron S

    2010-08-01

    Full Text Available Abstract Background The mini-chromosome maintenance protein (MCM complex is an essential replicative helicase for DNA replication in Archaea and Eukaryotes. While the eukaryotic complex consists of six homologous proteins (MCM2-7, the archaeon Sulfolobus solfataricus has only one MCM protein (ssoMCM, six subunits of which form a homohexamer. We have recently reported a 4.35Å crystal structure of the near full-length ssoMCM. The structure reveals a total of four β-hairpins per subunit, three of which are located within the main channel or side channels of the ssoMCM hexamer model generated based on the symmetry of the N-terminal Methanothermobacter thermautotrophicus (mtMCM structure. The fourth β-hairpin, however, is located on the exterior of the hexamer, near the exit of the putative side channels and next to the ATP binding pocket. Results In order to better understand this hairpin's role in DNA binding and helicase activity, we performed a detailed mutational and biochemical analysis of nine residues on this exterior β-hairpin (EXT-hp. We examined the activities of the mutants related to their helicase function, including hexamerization, ATPase, DNA binding and helicase activities. The assays showed that some of the residues on this EXT-hp play a role for DNA binding as well as for helicase activity. Conclusions These results implicate several current theories regarding helicase activity by this critical hexameric enzyme. As the data suggest that EXT-hp is involved in DNA binding, the results reported here imply that the EXT-hp located near the exterior exit of the side channels may play a role in contacting DNA substrate in a manner that affects DNA unwinding.

  7. Overcoming natural replication barriers: differential helicase requirements.

    Science.gov (United States)

    Anand, Ranjith P; Shah, Kartik A; Niu, Hengyao; Sung, Patrick; Mirkin, Sergei M; Freudenreich, Catherine H

    2012-02-01

    DNA sequences that form secondary structures or bind protein complexes are known barriers to replication and potential inducers of genome instability. In order to determine which helicases facilitate DNA replication across these barriers, we analyzed fork progression through them in wild-type and mutant yeast cells, using 2-dimensional gel-electrophoretic analysis of the replication intermediates. We show that the Srs2 protein facilitates replication of hairpin-forming CGG/CCG repeats and prevents chromosome fragility at the repeat, whereas it does not affect replication of G-quadruplex forming sequences or a protein-bound repeat. Srs2 helicase activity is required for hairpin unwinding and fork progression. Also, the PCNA binding domain of Srs2 is required for its in vivo role of replication through hairpins. In contrast, the absence of Sgs1 or Pif1 helicases did not inhibit replication through structural barriers, though Pif1 did facilitate replication of a telomeric protein barrier. Interestingly, replication through a protein barrier but not a DNA structure barrier was modulated by nucleotide pool levels, illuminating a different mechanism by which cells can regulate fork progression through protein-mediated stall sites. Our analyses reveal fundamental differences in the replication of DNA structural versus protein barriers, with Srs2 helicase activity exclusively required for fork progression through hairpin structures.

  8. Alfalfa stem tissues: Cell wall deposition, composition, and degradability

    NARCIS (Netherlands)

    Jung, H.G.; Engels, F.M.

    2002-01-01

    Declining cell wall degradability of alfalfa (Medicago sativa L.) stems with maturation limits the nutritional value of alfalfa for ruminants. This study characterized changes in cell wall concentration, composition, and degradability by rumen microbes resulting from alfalfa stem tissue

  9. Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing

    Directory of Open Access Journals (Sweden)

    Li Xuehui

    2012-10-01

    Full Text Available Abstract Background Alfalfa, a perennial, outcrossing species, is a widely planted forage legume producing highly nutritious biomass. Currently, improvement of cultivated alfalfa mainly relies on recurrent phenotypic selection. Marker assisted breeding strategies can enhance alfalfa improvement efforts, particularly if many genome-wide markers are available. Transcriptome sequencing enables efficient high-throughput discovery of single nucleotide polymorphism (SNP markers for a complex polyploid species. Result The transcriptomes of 27 alfalfa genotypes, including elite breeding genotypes, parents of mapping populations, and unimproved wild genotypes, were sequenced using an Illumina Genome Analyzer IIx. De novo assembly of quality-filtered 72-bp reads generated 25,183 contigs with a total length of 26.8 Mbp and an average length of 1,065 bp, with an average read depth of 55.9-fold for each genotype. Overall, 21,954 (87.2% of the 25,183 contigs represented 14,878 unique protein accessions. Gene ontology (GO analysis suggested that a broad diversity of genes was represented in the resulting sequences. The realignment of individual reads to the contigs enabled the detection of 872,384 SNPs and 31,760 InDels. High resolution melting (HRM analysis was used to validate 91% of 192 putative SNPs identified by sequencing. Both allelic variants at about 95% of SNP sites identified among five wild, unimproved genotypes are still present in cultivated alfalfa, and all four US breeding programs also contain a high proportion of these SNPs. Thus, little evidence exists among this dataset for loss of significant DNA sequence diversity from either domestication or breeding of alfalfa. Structure analysis indicated that individuals from the subspecies falcata, the diploid subspecies caerulea, and the tetraploid subspecies sativa (cultivated tetraploid alfalfa were clearly separated. Conclusion We used transcriptome sequencing to discover large numbers of SNPs

  10. Isolation and Characterization of Pepper Genes Interacting with the CMV-P1 Helicase Domain.

    Directory of Open Access Journals (Sweden)

    Yoomi Choi

    Full Text Available Cucumber mosaic virus (CMV is a destructive pathogen affecting Capsicum annuum (pepper production. The pepper Cmr1 gene confers resistance to most CMV strains, but is overcome by CMV-P1 in a process dependent on the CMV-P1 RNA1 helicase domain (P1 helicase. Here, to identify host factors involved in CMV-P1 infection in pepper, a yeast two-hybrid library derived from a C. annuum 'Bukang' cDNA library was screened, producing a total of 76 potential clones interacting with the P1 helicase. Beta-galactosidase filter lift assay, PCR screening, and sequencing analysis narrowed the candidates to 10 genes putatively involved in virus infection. The candidate host genes were silenced in Nicotiana benthamiana plants that were then inoculated with CMV-P1 tagged with the green fluorescent protein (GFP. Plants silenced for seven of the genes showed development comparable to N. benthamiana wild type, whereas plants silenced for the other three genes showed developmental defects including stunting and severe distortion. Silencing formate dehydrogenase and calreticulin-3 precursor led to reduced virus accumulation. Formate dehydrogenase-silenced plants showed local infection in inoculated leaves, but not in upper (systemic leaves. In the calreticulin-3 precursor-silenced plants, infection was not observed in either the inoculated or the upper leaves. Our results demonstrate that formate dehydrogenase and calreticulin-3 precursor are required for CMV-P1 infection.

  11. The Arabidopsis thaliana homolog of the helicase RTEL1 plays multiple roles in preserving genome stability.

    Science.gov (United States)

    Recker, Julia; Knoll, Alexander; Puchta, Holger

    2014-12-01

    In humans, mutations in the DNA helicase Regulator of Telomere Elongation Helicase1 (RTEL1) lead to Hoyeraal-Hreidarsson syndrome, a severe, multisystem disorder. Here, we demonstrate that the RTEL1 homolog in Arabidopsis thaliana plays multiple roles in preserving genome stability. RTEL1 suppresses homologous recombination in a pathway parallel to that of the DNA translocase FANCM. Cytological analyses of root meristems indicate that RTEL1 is involved in processing DNA replication intermediates independently from FANCM and the nuclease MUS81. Moreover, RTEL1 is involved in interstrand and intrastrand DNA cross-link repair independently from FANCM and (in intrastrand cross-link repair) parallel to MUS81. RTEL1 contributes to telomere homeostasis; the concurrent loss of RTEL1 and the telomerase TERT leads to rapid, severe telomere shortening, which occurs much more rapidly than it does in the single-mutant line tert, resulting in developmental arrest after four generations. The double mutant rtel1-1 recq4A-4 exhibits massive growth defects, indicating that this RecQ family helicase, which is also involved in the suppression of homologous recombination and the repair of DNA lesions, can partially replace RTEL1 in the processing of DNA intermediates. The requirement for RTEL1 in multiple pathways to preserve genome stability in plants can be explained by its putative role in the destabilization of DNA loop structures, such as D-loops and T-loops. © 2014 American Society of Plant Biologists. All rights reserved.

  12. Genetic Engineering of Alfalfa (Medicago sativa L.).

    Science.gov (United States)

    Wang, Dan; Khurshid, Muhammad; Sun, Zhan Min; Tang, Yi Xiong; Zhou, Mei Liang; Wu, Yan Min

    2016-01-01

    Alfalfa is excellent perennial legume forage for its extensive ecological adaptability, high nutrition value, palatability and biological nitrogen fixation. It plays a very important role in the agriculture, animal husbandry and ecological construction. It is cultivated in all continents. With the development of modern plant breeding and genetic engineering techniques, a large amount of work has been carried out on alfalfa. Here we summarize the recent research advances in genetic engineering of alfalfa breeding, including transformation, quality improvement, stress resistance and as a bioreactor. The review article can enables us to understand the research method, direction and achievements of genetic engineering technology of Alfalfa.

  13. A Co-Opted DEAD-Box RNA helicase enhances tombusvirus plus-strand synthesis.

    Directory of Open Access Journals (Sweden)

    Nikolay Kovalev

    2012-02-01

    Full Text Available Replication of plus-strand RNA viruses depends on recruited host factors that aid several critical steps during replication. In this paper, we show that an essential translation factor, Ded1p DEAD-box RNA helicase of yeast, directly affects replication of Tomato bushy stunt virus (TBSV. To separate the role of Ded1p in viral protein translation from its putative replication function, we utilized a cell-free TBSV replication assay and recombinant Ded1p. The in vitro data show that Ded1p plays a role in enhancing plus-strand synthesis by the viral replicase. We also find that Ded1p is a component of the tombusvirus replicase complex and Ded1p binds to the 3'-end of the viral minus-stranded RNA. The data obtained with wt and ATPase deficient Ded1p mutants support the model that Ded1p unwinds local structures at the 3'-end of the TBSV (-RNA, rendering the RNA compatible for initiation of (+-strand synthesis. Interestingly, we find that Ded1p and glyceraldehyde-3-phosphate dehydrogenase (GAPDH, which is another host factor for TBSV, play non-overlapping functions to enhance (+-strand synthesis. Altogether, the two host factors enhance TBSV replication synergistically by interacting with the viral (-RNA and the replication proteins. In addition, we have developed an in vitro assay for Flock house virus (FHV, a small RNA virus of insects, that also demonstrated positive effect on FHV replicase activity by the added Ded1p helicase. Thus, two small RNA viruses, which do not code for their own helicases, seems to recruit a host RNA helicase to aid their replication in infected cells.

  14. [RTEL1 (regulator of telomere elongation helicase 1), a DNA helicase essential for genome stability].

    Science.gov (United States)

    Le Guen, Tangui; Jullien, Laurent; Schertzer, Mike; Lefebvre, Axelle; Kermasson, Laetitia; de Villartay, Jean-Pierre; Londoño-Vallejo, Arturo; Revy, Patrick

    2013-12-01

    RTEL1 (regulator of telomere length helicase 1) is a DNA helicase that has been identified more than 10 years ago. Many works since, mainly in the nematode Caenorhabditis elegans and the mouse, have highlighted its role in chromosomal stability, maintenance of telomere length, and DNA repair. Recently, four laboratories have characterized RTEL1 mutations in patients with dyskeratosis congenita (DC) and Hoyeraal-Hreidarsson (HH) syndrome, a rare and severe variant of DC. We here summarize the current knowledge on RTEL1 and discuss the possible other functions that RTEL1 could play. © 2013 médecine/sciences – Inserm.

  15. Alfalfa virus S, a new species in the family Alphaflexiviridae.

    Directory of Open Access Journals (Sweden)

    Lev G Nemchinov

    Full Text Available A new species of the family Alphaflexiviridae provisionally named alfalfa virus S (AVS was discovered in alfalfa samples originating from Sudan. A complete nucleotide sequence of the viral genome consisting of 8,349 nucleotides excluding the 3' poly(A tail was determined by high throughput sequencing (HTS on an Illumina platform. NCBI BLAST searches revealed that the virus shares the greatest degree of sequence identity with members of the family Alphaflexiviridae, genus Allexivirus. The AVS genome contains six computationally-predicted open reading frames (ORF encoding viral replication protein, triple gene block protein 1 (TGB1, TGB2, TGB3-like protein, unknown 38.4 kDa protein resembling serine-rich 40 kDa protein characteristic for allexiviruses, and coat protein (CP. AVS lacks a clear 3' proximal ORF that encodes a nucleic acid-binding protein typical for allexiviruses. The identity of the virus was confirmed by RT-PCR with primers derived from the HTS-generated sequence, dot blot hybridization with DIG-labeled virus-specific RNA probes, and Western blot analysis with antibodies produced against a peptide derived from the CP sequence. Transmission electron microscopic observations of the infected tissues showed the presence of filamentous particles similar to allexiviruses in their length and appearance. To the best of our knowledge, this is the first report on the identification of a putative allexivirus in alfalfa (Medicago sativa. The genome sequence of AVS has been deposited in NCBI GenBank on 03/02/2016 as accession № KY696659.

  16. Crystal structure of Middle East respiratory syndrome coronavirus helicase.

    Directory of Open Access Journals (Sweden)

    Wei Hao

    2017-06-01

    Full Text Available Middle East respiratory syndrome coronavirus (MERS-CoV remains a threat to public health worldwide; however, effective vaccine or drug against CoVs remains unavailable. CoV helicase is one of the three evolutionary most conserved proteins in nidoviruses, thus making it an important target for drug development. We report here the first structure of full-length coronavirus helicase, MERS-CoV nsp13. MERS-CoV helicase has multiple domains, including an N-terminal Cys/His rich domain (CH with three zinc atoms, a beta-barrel domain and a C-terminal SF1 helicase core with two RecA-like subdomains. Our structural analyses show that while the domain organization of nsp13 is conserved throughout nidoviruses, the individual domains of nsp13 are closely related to the equivalent eukaryotic domains of Upf1 helicases. The most distinctive feature differentiating CoV helicases from eukaryotic Upf1 helicases is the interaction between CH domain and helicase core.

  17. Structural basis of Zika virus helicase in recognizing its substrates

    Directory of Open Access Journals (Sweden)

    Hongliang Tian

    2016-07-01

    Full Text Available Abstract The recent explosive outbreak of Zika virus (ZIKV infection has been reported in South and Central America and the Caribbean. Neonatal microcephaly associated with ZIKV infection has already caused a public health emergency of international concern. No specific vaccines or drugs are currently available to treat ZIKV infection. The ZIKV helicase, which plays a pivotal role in viral RNA replication, is an attractive target for therapy. We determined the crystal structures of ZIKV helicase-ATP-Mn2+ and ZIKV helicase-RNA. This is the first structure of any flavivirus helicase bound to ATP. Comparisons with related flavivirus helicases have shown that although the critical P-loop in the active site has variable conformations among different species, it adopts an identical mode to recognize ATP/Mn2+. The structure of ZIKV helicase-RNA has revealed that upon RNA binding, rotations of the motor domains can cause significant conformational changes. Strikingly, although ZIKV and dengue virus (DENV apo-helicases share conserved residues for RNA binding, their different manners of motor domain rotations result in distinct individual modes for RNA recognition. It suggests that flavivirus helicases could have evolved a conserved engine to convert chemical energy from nucleoside triphosphate to mechanical energy for RNA unwinding, but different motor domain rotations result in variable RNA recognition modes to adapt to individual viral replication.

  18. Applied Genetics and Genomics in Alfalfa Breeding

    Directory of Open Access Journals (Sweden)

    E. Charles Brummer

    2012-03-01

    Full Text Available Alfalfa (Medicago sativa L., a perennial and outcrossing species, is a widely planted forage legume for hay, pasture and silage throughout the world. Currently, alfalfa breeding relies on recurrent phenotypic selection, but alternatives incorporating molecular marker assisted breeding could enhance genetic gain per unit time and per unit cost, and accelerate alfalfa improvement. Many major quantitative trait loci (QTL related to agronomic traits have been identified by family-based QTL mapping, but in relatively large genomic regions. Candidate genes elucidated from model species have helped to identify some potential causal loci in alfalfa mapping and breeding population for specific traits. Recently, high throughput sequencing technologies, coupled with advanced bioinformatics tools, have been used to identify large numbers of single nucleotide polymorphisms (SNP in alfalfa, which are being developed into markers. These markers will facilitate fine mapping of quantitative traits and genome wide association mapping of agronomic traits and further advanced breeding strategies for alfalfa, such as marker-assisted selection and genomic selection. Based on ideas from the literature, we suggest several ways to improve selection in alfalfa including (1 diversity selection and paternity testing, (2 introgression of QTL and (3 genomic selection.

  19. Structural basis for the function of DEAH helicases

    DEFF Research Database (Denmark)

    He, Yangzi; Andersen, Gregers Rom; Nielsen, Klaus Hvid

    2010-01-01

    DEAH helicases participate in pre‐messenger RNA splicing and ribosome biogenesis. The structure of yeast Prp43p‐ADP reveals the homology of DEAH helicases to DNA helicases and the presence of an oligonucleotide‐binding motif. A β‐hairpin from the second RecA domain is wedged between two carboxy......‐terminal domains and blocks access to the occluded RNA binding site formed by the RecA domains and a C‐terminal domain. ATP binding and hydrolysis are likely to induce conformational changes in the hairpin that are important for RNA unwinding or ribonucleoprotein remodelling. The structure of Prp43p provides...

  20. Analysis of physiological and miRNA responses to Pi deficiency in alfalfa (Medicago sativa L.).

    Science.gov (United States)

    Li, Zhenyi; Xu, Hongyu; Li, Yue; Wan, Xiufu; Ma, Zhao; Cao, Jing; Li, Zhensong; He, Feng; Wang, Yufei; Wan, Liqiang; Tong, Zongyong; Li, Xianglin

    2018-03-01

    The induction of miR399 and miR398 and the inhibition of miR156, miR159, miR160, miR171, miR2111, and miR2643 were observed under Pi deficiency in alfalfa. The miRNA-mediated genes involved in basic metabolic process, root and shoot development, stress response and Pi uptake. Inorganic phosphate (Pi) deficiency is known to be a limiting factor in plant development and growth. However, the underlying miRNAs associated with the Pi deficiency-responsive mechanism in alfalfa are unclear. To elucidate the molecular mechanism at the miRNA level, we constructed four small RNA (sRNA) libraries from the roots and shoots of alfalfa grown under normal or Pi-deficient conditions. In the present study, alfalfa plants showed reductions in biomass, photosynthesis, and Pi content and increases in their root-to-shoot ratio and citric, malic, and succinic acid contents under Pi limitation. Sequencing results identified 47 and 44 differentially expressed miRNAs in the roots and shoots, respectively. Furthermore, 909 potential target genes were predicted, and some targets were validated by RLM-RACE assays. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed prominent enrichment in signal transducer activity, binding and basic metabolic pathways for carbohydrates, fatty acids and amino acids; cellular response to hormone stimulus and response to auxin pathways were also enriched. qPCR results verified that the differentially expressed miRNA profile was consistent with sequencing results, and putative target genes exhibited opposite expression patterns. In this study, the miRNAs associated with the response to Pi limitation in alfalfa were identified. In addition, there was an enrichment of miRNA-targeted genes involved in biological regulatory processes such as basic metabolic pathways, root and shoot development, stress response, Pi transportation and citric acid secretion.

  1. Investigating the origin of the Chinese name for alfalfa

    Science.gov (United States)

    Sun, Q. Z.; Xu, L. J.; Tang, X. J.; Ma, J. T.; Wang, D.; Li, D.; Liu, Q.; Tao, Y.; Li, F.

    2017-02-01

    It is assured that alfalfa (Medicago sativa L.) was introduced in Han dynasty. There are cognitive differences on whether Zhang Qian introduced alfalfa. Based on the previous studies, research inductive method was used. The relationship between Zhang Qian and alfalfa introduction was analyzed from the motivation, experience and influence of Zhang Qian to the Western Regions and the image generation of Zhang Qian brought back alfalfa’s seeds. Till to now, there are four opinions about Zhang Qian introducing Alfalfa seeds, including : (1) Zhang Qian introduced alfalfa seeds;(2) Zhang Qian did not introduce alfalfa seeds;(3) the information of Zhang Qian transferring alfalfa;(4)for commemoration Zhang Qian to the Western Regions. Although there are not direct historical materials to support Zhang Qian brought alfalfa seed to Han dynasty, it believes and confirms that the introducing of alfalfa is inextricably interwoven with Zhang Qian’s western travel. Zhangqian brought relative information from western regions during the introduction, which was the basis of non-native theory, and after that, Chinese began to plant alfalfa in Han dynasty., According to historical literatures, it is clear that the Chinese diplomat brought alfalfa seeds back to China. Alfalfa, as the favorite forage to Ferghana horse, have been already planted in Dawan in Han dynasty. Despite the debate, Zhangqian played an important pioneering role in introducing alfalfa.

  2. The Arabidopsis thaliana Homolog of the Helicase RTEL1 Plays Multiple Roles in Preserving Genome Stability[C][W

    Science.gov (United States)

    Recker, Julia; Knoll, Alexander; Puchta, Holger

    2014-01-01

    In humans, mutations in the DNA helicase Regulator of Telomere Elongation Helicase1 (RTEL1) lead to Hoyeraal-Hreidarsson syndrome, a severe, multisystem disorder. Here, we demonstrate that the RTEL1 homolog in Arabidopsis thaliana plays multiple roles in preserving genome stability. RTEL1 suppresses homologous recombination in a pathway parallel to that of the DNA translocase FANCM. Cytological analyses of root meristems indicate that RTEL1 is involved in processing DNA replication intermediates independently from FANCM and the nuclease MUS81. Moreover, RTEL1 is involved in interstrand and intrastrand DNA cross-link repair independently from FANCM and (in intrastrand cross-link repair) parallel to MUS81. RTEL1 contributes to telomere homeostasis; the concurrent loss of RTEL1 and the telomerase TERT leads to rapid, severe telomere shortening, which occurs much more rapidly than it does in the single-mutant line tert, resulting in developmental arrest after four generations. The double mutant rtel1-1 recq4A-4 exhibits massive growth defects, indicating that this RecQ family helicase, which is also involved in the suppression of homologous recombination and the repair of DNA lesions, can partially replace RTEL1 in the processing of DNA intermediates. The requirement for RTEL1 in multiple pathways to preserve genome stability in plants can be explained by its putative role in the destabilization of DNA loop structures, such as D-loops and T-loops. PMID:25516598

  3. Mycobacterium smegmatis SftH exemplifies a distinctive clade of superfamily II DNA-dependent ATPases with 3' to 5' translocase and helicase activities.

    Science.gov (United States)

    Yakovleva, Lyudmila; Shuman, Stewart

    2012-08-01

    Bacterial DNA helicases are nucleic acid-dependent NTPases that play important roles in DNA replication, recombination and repair. We are interested in the DNA helicases of Mycobacteria, a genus of the phylum Actinobacteria, which includes the human pathogen Mycobacterium tuberculosis and its avirulent relative Mycobacterium smegmatis. Here, we identify and characterize M. smegmatis SftH, a superfamily II helicase with a distinctive domain structure, comprising an N-terminal NTPase domain and a C-terminal DUF1998 domain (containing a putative tetracysteine metal-binding motif). We show that SftH is a monomeric DNA-dependent ATPase/dATPase that translocates 3' to 5' on single-stranded DNA and has 3' to 5' helicase activity. SftH homologs are found in bacteria representing 12 different phyla, being especially prevalent in Actinobacteria (including M. tuberculosis). SftH homologs are evident in more than 30 genera of Archaea. Among eukarya, SftH homologs are present in plants and fungi.

  4. Preliminary crystallographic characterization of an RNA helicase from Kunjin virus

    International Nuclear Information System (INIS)

    Mastrangelo, Eloise; Bollati, Michela; Milani, Mario; Brisbarre, Nadège; Lamballerie, Xavier de; Coutard, Bruno; Canard, Bruno; Khromykh, Alexander; Bolognesi, Martino

    2006-01-01

    The C-terminal 440 amino acids of the NS3 protein from Kunjin virus (Flaviviridae) code for a helicase. The protein has been overexpressed and crystallized. Characterization of the isolated monoclinic crystal form and diffraction data (at 3.0 Å resolution) are presented, together with a preliminary molecular-replacement solution. Kunjin virus is a member of the Flavivirus genus and is an Australian variant of West Nile virus. The C-terminal domain of the Kunjin virus NS3 protein displays helicase activity. The protein is thought to separate daughter and template RNA strands, assisting the initiation of replication by unwinding RNA secondary structure in the 3′ nontranslated region. Expression, purification and preliminary crystallographic characterization of the NS3 helicase domain are reported. It is shown that Kunjin virus helicase may adopt a dimeric assembly in absence of nucleic acids, oligomerization being a means to provide the helicases with multiple nucleic acid-binding capability, facilitating translocation along the RNA strands. Kunjin virus NS3 helicase domain is an attractive model for studying the molecular mechanisms of flavivirus replication, while simultaneously providing a new basis for the rational development of anti-flaviviral compounds

  5. Mutants of alfalfa mosaic virus

    International Nuclear Information System (INIS)

    Roosien, J.

    1983-01-01

    In this thesis the isolation and characterization of a number of mutants of alfalfa mosaic virus, a plant virus with a coat protein dependent genome, is described. Thermo-sensitive (ts) mutants were selected since, at least theoretically, ts mutations can be present in all virus coded functions. It was found that a high percentage of spontaneous mutants, isolated because of their aberrant symptoms, were ts. The majority of these isolates could grow at the non-permissive temperature in the presence of a single wild type (wt) component. To increase the mutation rate virus preparations were treated with several mutagens. After nitrous acid treatment or irradiation with ultraviolet light, an increase in the level of mutations was observed. UV irradiation was preferred since it did not require large amounts of purified viral components. During the preliminary characterization of potential ts mutants the author also obtained one structural and several symptom mutants which were analysed further (chapter 7, 8 and 9). The properties of the ts mutants are described in chapter 3-7. (Auth.)

  6. DNA-conjugated gold nanoparticles based colorimetric assay to assess helicase activity: a novel route to screen potential helicase inhibitors

    Science.gov (United States)

    Deka, Jashmini; Mojumdar, Aditya; Parisse, Pietro; Onesti, Silvia; Casalis, Loredana

    2017-03-01

    Helicase are essential enzymes which are widespread in all life-forms. Due to their central role in nucleic acid metabolism, they are emerging as important targets for anti-viral, antibacterial and anti-cancer drugs. The development of easy, cheap, fast and robust biochemical assays to measure helicase activity, overcoming the limitations of the current methods, is a pre-requisite for the discovery of helicase inhibitors through high-throughput screenings. We have developed a method which exploits the optical properties of DNA-conjugated gold nanoparticles (AuNP) and meets the required criteria. The method was tested with the catalytic domain of the human RecQ4 helicase and compared with a conventional FRET-based assay. The AuNP-based assay produced similar results but is simpler, more robust and cheaper than FRET. Therefore, our nanotechnology-based platform shows the potential to provide a useful alternative to the existing conventional methods for following helicase activity and to screen small-molecule libraries as potential helicase inhibitors.

  7. Progress on researches of transgenic alfalfa

    International Nuclear Information System (INIS)

    Guo Huiqin; Wang Mi; Ren Weibo; Xu Zhu; Chen Libo

    2010-01-01

    In this paper, the progress on the researches of transgenic alfalfa in the past two decades had been reviewed in the aspects of regeneration system, transformation, improvement of the important traits and so on. Moreover, such problems as variation of transgene expression and safety of transgenic plant had also been discussed and propose had been given for the future research work. (authors)

  8. A conserved helicase processivity factor is needed for conjugation and replication of an integrative and conjugative element.

    Directory of Open Access Journals (Sweden)

    Jacob Thomas

    Full Text Available Integrative and conjugative elements (ICEs are agents of horizontal gene transfer and have major roles in evolution and acquisition of new traits, including antibiotic resistances. ICEs are found integrated in a host chromosome and can excise and transfer to recipient bacteria via conjugation. Conjugation involves nicking of the ICE origin of transfer (oriT by the ICE-encoded relaxase and transfer of the nicked single strand of ICE DNA. For ICEBs1 of Bacillus subtilis, nicking of oriT by the ICEBs1 relaxase NicK also initiates rolling circle replication. This autonomous replication of ICEBs1 is critical for stability of the excised element in growing cells. We found a conserved and previously uncharacterized ICE gene that is required for conjugation and replication of ICEBs1. Our results indicate that this gene, helP (formerly ydcP, encodes a helicase processivity factor that enables the host-encoded helicase PcrA to unwind the double-stranded ICEBs1 DNA. HelP was required for both conjugation and replication of ICEBs1, and HelP and NicK were the only ICEBs1 proteins needed for replication from ICEBs1 oriT. Using chromatin immunoprecipitation, we measured association of HelP, NicK, PcrA, and the host-encoded single-strand DNA binding protein Ssb with ICEBs1. We found that NicK was required for association of HelP and PcrA with ICEBs1 DNA. HelP was required for association of PcrA and Ssb with ICEBs1 regions distal, but not proximal, to oriT, indicating that PcrA needs HelP to progress beyond nicked oriT and unwind ICEBs1. In vitro, HelP directly stimulated the helicase activity of the PcrA homologue UvrD. Our findings demonstrate that HelP is a helicase processivity factor needed for efficient unwinding of ICEBs1 for conjugation and replication. Homologues of HelP and PcrA-type helicases are encoded on many known and putative ICEs. We propose that these factors are essential for ICE conjugation, replication, and genetic stability.

  9. Viral hijacking of a replicative helicase loader and its implications for helicase loading control and phage replication

    Energy Technology Data Exchange (ETDEWEB)

    Hood, Iris V.; Berger, James M.

    2016-05-31

    Replisome assembly requires the loading of replicative hexameric helicases onto origins by AAA+ ATPases. How loader activity is appropriately controlled remains unclear. Here, we use structural and biochemical analyses to establish how an antimicrobial phage protein interferes with the function of theStaphylococcus aureusreplicative helicase loader, DnaI. The viral protein binds to the loader’s AAA+ ATPase domain, allowing binding of the host replicative helicase but impeding loader self-assembly and ATPase activity. Close inspection of the complex highlights an unexpected locus for the binding of an interdomain linker element in DnaI/DnaC-family proteins. We find that the inhibitor protein is genetically coupled to a phage-encoded homolog of the bacterial helicase loader, which we show binds to the host helicase but not to the inhibitor itself. These findings establish a new approach by which viruses can hijack host replication processes and explain how loader activity is internally regulated to prevent aberrant auto-association.

  10. RecQ helicases and cellular responses to DNA damage

    International Nuclear Information System (INIS)

    Wu, Leonard; Hickson, Ian D.

    2002-01-01

    The faithful replication of the genome is essential for the survival of all organisms. It is not surprising therefore that numerous mechanisms have evolved to ensure that duplication of the genome occurs with only minimal risk of mutation induction. One mechanism of genome destabilization is replication fork demise, which can occur when a translocating fork meets a lesion or adduct in the template. Indeed, the collapse of replication forks has been suggested to occur in every replicative cell cycle making this a potentially significant problem for all proliferating cells. The RecQ helicases, which are essential for the maintenance of genome stability, are thought to function during DNA replication. In particular, RecQ helicase mutants display replication defects and have phenotypes consistent with an inability to efficiently reinitiate replication following replication fork demise. Here, we review some current models for how replication fork repair might be effected, and discuss potential roles for RecQ helicases in this process

  11. [Soil dryness characteristics of alfalfa cropland and optimal growth years of alfalfa on the Loess Plateau of central Gansu, China].

    Science.gov (United States)

    Luo, Zhu-zhu; Li, Ling-ling; Niu, Yi-ning; Cai, Li-qun; Zhang, Ren-zhi; Xie, Jun-hong

    2015-10-01

    This paper investigated soil moisture in alfalfa (Medicago sativa) cropland with different growth years (1, 3, 8, 12 and 14 years) and discussed the optimum growth years of alfalfa on the Loess Plateau of central Gansu. The results showed that the soil moisture along 0-300 cm soil profile of alfalfa croplands with different growth years was obviously lower than that of the local soil stable moisture. The soil water contents in croplands with alfalfa that had grown for 12 and 14 years were only 9.2% and 7.1% of local soil stable moisture, respectively, which were even lower than the lower limit of alfalfa growth. The average soil dryness indexes along 0-300 cm soil profile in 1, 3, 8, 12 and 14 years alfalfa croplands were 125.4%, 30.5%, 18.4%, -34.2% and -83.3% respectively. The results indicated that soil dryness occurred to varying degrees with different growth years except croplands with alfalfa grown for 1 year. With the increase of growth years of alfalfa, the soil dryness intensity increased and the soil dryness rate decreased. According to the soil moisture and alfalfa productivity results in this study, it could be concluded that the optimum growth years of alfalfa are 8-10 years in semiarid areas of the Loess Plateau.

  12. Health status of alfalfa leafcutting bee larvae (Hymenoptera: Megachilidae) in United States alfalfa seed fields.

    Science.gov (United States)

    James, R R; Pitts-Singer, T L

    2013-12-01

    We conducted a broad geographic survey in the northwestern United States to quantify production losses in the alfalfa leafcutting bee (Megachile rotundata (F.), Hymenoptera: Megachilidae), a solitary pollinator used extensively in alfalfa seed production. Viable larvae were found in only 47.1% of the nest cells collected at the end of the season. Most of the rest of the cells contained pollen balls (typified by a provision but no larva; 16.7%), unknown causes of mortality (15.5%), or larvae killed by chalkbrood (8.0%). Prevalence of pollen balls was correlated positively with bee release rates and negatively with alfalfa stand age. The unknown mortality was correlated with the U.S. Department of Agriculture-Plant Hardiness Zone, and thus, some of the mortality may be caused by high temperature extremes, although the nesting season degree-days were not correlated with this mortality. Chalkbrood prevalence was correlated with possible nesting-resource or crowding-related factors, such as the number of bees released per hectare and the number of shelters used, but not with nesting board disinfection practices. Vapona is used to control parasitoids when the parent bees are incubated before release, and use of this fumigant was associated with an increase in both chalkbrood and diapausing offspring, although any reason for these correlations are unknown. This survey quantifies the variation in the quality of alfalfa leafcutting bee cocoons produced across much of the U.S. alfalfa seed production area.

  13. Efficiency of alfalfa seed processing with different seed purity

    OpenAIRE

    Đokić, Dragoslav; Stanisavljević, Rade; Terzić, Dragan; Milenković, Jasmina; Radivojević, Gordana; Koprivica, Ranko; Štrbanović, Ratibor

    2015-01-01

    The work was carried out analysis of the impact of the initial purity of raw alfalfa seed on the resulting amount of processed seed in the processing. Alfalfa is very important perennial forage legume which is used for fodder and seed production. Alfalfa seed is possible to achieve high yields and very good financial effects. To obtain the seed material with good characteristics complex machines for cleaning and sorting seeds are used. In the processing center of the Institute for forage crop...

  14. Alfalfa breeding benefits from genomics of Medicago truncatula

    Directory of Open Access Journals (Sweden)

    Žilije Bernadet

    2010-01-01

    Full Text Available International programs aim at developing knowledge and tools in the model species Medicago truncatula. Genetic resources, DNA sequences, markers, genetic and physical maps are now publicly available. These efforts contribute to improve breeding schemes of crop species such as alfalfa. However, transfer of information from M. truncatula to alfalfa is not straightforward. The article reviews the gain given by the model species to better analyze genetic determinism of breeding traits in alfalfa. It also shows that investments in alfalfa genomics (DNA sequences, SNP development are needed to benefit from the model species.

  15. MCM Paradox: Abundance of Eukaryotic Replicative Helicases and Genomic Integrity.

    Science.gov (United States)

    Das, Mitali; Singh, Sunita; Pradhan, Satyajit; Narayan, Gopeshwar

    2014-01-01

    As a crucial component of DNA replication licensing system, minichromosome maintenance (MCM) 2-7 complex acts as the eukaryotic DNA replicative helicase. The six related MCM proteins form a heterohexamer and bind with ORC, CDC6, and Cdt1 to form the prereplication complex. Although the MCMs are well known as replicative helicases, their overabundance and distribution patterns on chromatin present a paradox called the "MCM paradox." Several approaches had been taken to solve the MCM paradox and describe the purpose of excess MCMs distributed beyond the replication origins. Alternative functions of these MCMs rather than a helicase had also been proposed. This review focuses on several models and concepts generated to solve the MCM paradox coinciding with their helicase function and provides insight into the concept that excess MCMs are meant for licensing dormant origins as a backup during replication stress. Finally, we extend our view towards the effect of alteration of MCM level. Though an excess MCM constituent is needed for normal cells to withstand stress, there must be a delineation of the threshold level in normal and malignant cells. This review also outlooks the future prospects to better understand the MCM biology.

  16. Stress responses in alfalfa (Medicago sativa L.)

    International Nuclear Information System (INIS)

    Kessmann, H.; Edwards, R.; Dixon, R.A.; Geno, P.W.

    1990-01-01

    The isoflavonoid conjugates medicarpin-3-O-glucoside-6 double-prime-O-malonate (MGM), afrormosin-7-O-glucoside (AG), and afrormosin-7-O-glucoside-6 double-prime-O-malonate (AGM) were isolated and characterized from cell suspension cultures of alfalfa (Medicago sativa L.), where they were the major constitutive secondary metabolites. They were also found in alfalfa roots but not in other parts of the plant. The phytoalexin medicarpin accumulated rapidly in suspension cultured cells treated with elicitor from Colletotrichum lindemuthianum, and this was subsequently accompanied by an increase in the levels of MGM. In contrast, net accumulation of afrormosin conjugates was not affected by elicitor treatment. Labeling studies with [ 14 C]phenylalanine indicated that afrormosin conjugates were the major de novo synthesized isoflavonoid products in unelicited cells. During elicitation, [ 14 C]phenylalanine was incorporated predominantly into medicarpin, although a significant proportion of the newly synthesized medicarpin was also conjugated. Treatment of 14 C-labeled, elicited cells with L-α-aminooxy-β-phenylpropionic acid, a potent inhibitor of PAL activity in vivo, resulted in the initial appearance of labeled medicarpin of very low specific activity, suggesting that the phytoalexin could be released from a preformed conjugate under these conditions. Our data draw attention to the involvement of isoflavone hydroxylases during the constitutive and elicitor-induced accumulation of isoflavonoids and their conjugates in alfalfa cell cultures

  17. Three-dimensional structure of N-terminal domain of DnaB helicase and helicase-primase interactions in Helicobacter pylori.

    Directory of Open Access Journals (Sweden)

    Tara Kashav

    2009-10-01

    Full Text Available Replication initiation is a crucial step in genome duplication and homohexameric DnaB helicase plays a central role in the replication initiation process by unwinding the duplex DNA and interacting with several other proteins during the process of replication. N-terminal domain of DnaB is critical for helicase activity and for DnaG primase interactions. We present here the crystal structure of the N-terminal domain (NTD of H. pylori DnaB (HpDnaB helicase at 2.2 A resolution and compare the structural differences among helicases and correlate with the functional differences. The structural details of NTD suggest that the linker region between NTD and C-terminal helicase domain plays a vital role in accurate assembly of NTD dimers. The sequence analysis of the linker regions from several helicases reveals that they should form four helix bundles. We also report the characterization of H. pylori DnaG primase and study the helicase-primase interactions, where HpDnaG primase stimulates DNA unwinding activity of HpDnaB suggesting presence of helicase-primase cohort at the replication fork. The protein-protein interaction study of C-terminal domain of primase and different deletion constructs of helicase suggests that linker is essential for proper conformation of NTD to interact strongly with HpDnaG. The surface charge distribution on the primase binding surface of NTDs of various helicases suggests that DnaB-DnaG interaction and stability of the complex is most probably charge dependent. Structure of the linker and helicase-primase interactions indicate that HpDnaB differs greatly from E.coli DnaB despite both belong to gram negative bacteria.

  18. Velocity and processivity of helicase unwinding of double-stranded nucleic acids

    International Nuclear Information System (INIS)

    Betterton, M D; Juelicher, F

    2005-01-01

    Helicases are molecular motors which unwind double-stranded nucleic acids (dsNA) in cells. Many helicases move with directional bias on single-stranded (ss) nucleic acids, and couple their directional translocation to strand separation. A model of the coupling between translocation and unwinding uses an interaction potential to represent passive and active helicase mechanisms. A passive helicase must wait for thermal fluctuations to open dsNA base pairs before it can advance and inhibit NA closing. An active helicase directly destabilizes dsNA base pairs, accelerating the opening rate. Here we extend this model to include helicase unbinding from the nucleic-acid strand. The helicase processivity depends on the form of the interaction potential. A passive helicase has a mean attachment time which does not change between ss translocation and ds unwinding, while an active helicase in general shows a decrease in attachment time during unwinding relative to ss translocation. In addition, we describe how helicase unwinding velocity and processivity vary if the base-pair binding free energy is changed

  19. Practices that support coexistence: A survey of Alfalfa growers

    Science.gov (United States)

    The alfalfa industry has worked hard to foster the coexistence of genetically-engineered (GE) and conventional alfalfa production by developing a set of best management practices that aim to limit adventitious-presence (AP) of GE traits in conventional seed. The general goal is to minimize transgene...

  20. Alfalfa virus S, a new species in the family Alphaflexiviridae

    Science.gov (United States)

    A new species of the family Alphaflexiviridae provisionally named alfalfa virus S (AVS) was discovered in alfalfa samples originating from Sudan. A complete nucleotide sequence of the viral genome consisting of 8,349 nucleotides excluding the 3’ poly(A) tail was determined by high throughput sequenc...

  1. Lessons learned in managing alfalfa-grass mixtures

    Science.gov (United States)

    Grass-alfalfa mixtures have a number of benefits that make them attractive to producers. However, they can be problematic to establish and maintain. Research programs have made progress in understanding the benefits and challenges of alfalfa-grass mixtures. Mixtures may have greater winter survival ...

  2. Water transfer in an alfalfa/maize association

    International Nuclear Information System (INIS)

    Corak, S.J.; Blevins, D.G.; Pallardy, S.G.

    1987-01-01

    The authors investigated the possibility of interspecific water transfer in an alfalfa (Medicago sativa L.) and maize (Zea mays L.) association. An alfalfa plant was grown through two vertically stacked plastic tubes. A 5 centimeter air gap between tubes was bridged by alfalfa roots. Five-week old maize plants with roots confined to the top tube were not watered, while associated alfalfa roots had free access to water in the bottom tube (the -/+ treatment). Additional treatments included: top and bottom tubes watered (+/+), top and bottom tubes droughted (-/-), and top tube droughted after removal of alfalfa root bridges and routine removal of alfalfa tillers (-*). Predawn leaf water potential of maize in the -/+ treatment fell to -1.5 megapascals 13 days after the start of drought; thereafter, predawn and midday potentials were maintained near -1.9 megapascals. Leaf water potentials of maize in the -/- and -* treatments declined steadily; all plants in these treatments were completely desiccated before day 50. High levels of tritium activity were detected in water extracted from both alfalfa and maize leaves after 3 H 2 O was injected into the bottom -/+ tube at day 70 or later. Maize in the -/+ treatment was able to survive an otherwise lethal period of drought by utilizing water lost by alfalfa roots

  3. Genome-Wide Association Study Identifies Loci for Salt Tolerance during Germination in Autotetraploid Alfalfa (Medicago sativa L.) Using Genotyping-by-Sequencing

    Science.gov (United States)

    Yu, Long-Xi; Liu, Xinchun; Boge, William; Liu, Xiang-Ping

    2016-01-01

    Salinity is one of major abiotic stresses limiting alfalfa (Medicago sativa L.) production in the arid and semi-arid regions in US and other counties. In this study, we used a diverse panel of alfalfa accessions previously described by Zhang et al. (2015) to identify molecular markers associated with salt tolerance during germination using genome-wide association study (GWAS) and genotyping-by-sequencing (GBS). Phenotyping was done by germinating alfalfa seeds under different levels of salt stress. Phenotypic data of adjusted germination rates and SNP markers generated by GBS were used for marker-trait association. Thirty six markers were significantly associated with salt tolerance in at least one level of salt treatments. Alignment of sequence tags to the Medicago truncatula genome revealed genetic locations of the markers on all chromosomes except chromosome 3. Most significant markers were found on chromosomes 1, 2, and 4. BLAST search using the flanking sequences of significant markers identified 14 putative candidate genes linked to 23 significant markers. Most of them were repeatedly identified in two or three salt treatments. Several loci identified in the present study had similar genetic locations to the reported QTL associated with salt tolerance in M. truncatula. A locus identified on chromosome 6 by this study overlapped with that by drought in our previous study. To our knowledge, this is the first report on mapping loci associated with salt tolerance during germination in autotetraploid alfalfa. Further investigation on these loci and their linked genes would provide insight into understanding molecular mechanisms by which salt and drought stresses affect alfalfa growth. Functional markers closely linked to the resistance loci would be useful for MAS to improve alfalfa cultivars with enhanced resistance to drought and salt stresses. PMID:27446182

  4. A Brownian motor mechanism of translocation and strand separation by hepatitis C virus helicase.

    Science.gov (United States)

    Levin, Mikhail K; Gurjar, Madhura; Patel, Smita S

    2005-05-01

    Helicases translocate along their nucleic acid substrates using the energy of ATP hydrolysis and by changing conformations of their nucleic acid-binding sites. Our goal is to characterize the conformational changes of hepatitis C virus (HCV) helicase at different stages of ATPase cycle and to determine how they lead to translocation. We have reported that ATP binding reduces HCV helicase affinity for nucleic acid. Now we identify the stage of the ATPase cycle responsible for translocation and unwinding. We show that a rapid directional movement occurs upon helicase binding to DNA in the absence of ATP, resulting in opening of several base pairs. We propose that HCV helicase translocates as a Brownian motor with a simple two-stroke cycle. The directional movement step is fueled by single-stranded DNA binding energy while ATP binding allows for a brief period of random movement that prepares the helicase for the next cycle.

  5. GINS complex protein Sld5 recruits SIK1 to activate MCM helicase during DNA replication.

    Science.gov (United States)

    Joshi, Kiranmai; Shah, Varun Jayeshkumar; Maddika, Subbareddy

    2016-12-01

    In eukaryotes, proper loading and activation of MCM helicase at chromosomal origins plays a central role in DNA replication. Activation of MCM helicase requires its association with CDC45-GINS complex, but the mechanism of how this complex activates MCM helicase is poorly understood. Here we identified SIK1 (salt-inducible kinase 1), an AMPK related protein kinase, as a molecular link that connects GINS complex with MCM helicase activity. We demonstrated that Sld5 a component of GINS complex interacts with SIK1 and recruits it to the sites of DNA replication at the onset of S phase. Depletion of SIK1 leads to defective DNA replication. Further, we showed that SIK1 phosphorylates MCM2 at five conserved residues at its N-terminus, which is essential for the activation of MCM helicase. Collectively, our results suggest SIK1 as a novel integral component of CMG replicative helicase during eukaryotic DNA replication. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Inhibition of RNA Helicases of ssRNA+ Virus Belonging to Flaviviridae, Coronaviridae and Picornaviridae Families

    Directory of Open Access Journals (Sweden)

    Irene Briguglio

    2011-01-01

    Full Text Available Many viral pathogens encode the motor proteins named RNA helicases which display various functions in genome replication. General strategies to design specific and selective drugs targeting helicase for the treatment of viral infections could act via one or more of the following mechanisms: inhibition of the NTPase activity, by interferences with ATP binding and therefore by limiting the energy required for the unwinding and translocation, or by allosteric mechanism and therefore by stabilizing the conformation of the enzyme in low helicase activity state; inhibition of nucleic acids binding to the helicase; inhibition of coupling of ATP hydrolysis to unwinding; inhibition of unwinding by sterically blocking helicase translocation. Recently, by in vitro screening studies, it has been reported that several benzotriazole, imidazole, imidazodiazepine, phenothiazine, quinoline, anthracycline, triphenylmethane, tropolone, pyrrole, acridone, small peptide, and Bananin derivatives are endowed with helicase inhibition of pathogen viruses belonging to Flaviviridae, Coronaviridae, and Picornaviridae families.

  7. Saccharomyces cerevisiae Hrq1 requires a long 3′-tailed DNA substrate for helicase activity

    International Nuclear Information System (INIS)

    Kwon, Sung-Hun; Choi, Do-Hee; Lee, Rina; Bae, Sung-Ho

    2012-01-01

    Highlights: ► Hrq1 has intrinsic 3′–5′ helicase and DNA strand annealing activities. ► Hrq1 requires a long 3′-tail for efficient DNA unwinding. ► Helicase activity of Hrq1 is stimulated by a fork structure. ► Hrq1 is a moderately processive helicase. -- Abstract: RecQ helicases are well conserved proteins from bacteria to human and function in various DNA metabolism for maintenance of genome stability. Five RecQ helicases are found in humans, whereas only one RecQ helicase has been described in lower eukaryotes. However, recent studies predicted the presence of a second RecQ helicase, Hrq1, in fungal genomes and verified it as a functional gene in fission yeast. Here we show that 3′–5′ helicase activity is intrinsically associated with Hrq1 of Saccharomyces cerevisiae. We also determined several biochemical properties of Hrq1 helicase distinguishable from those of other RecQ helicase members. Hrq1 is able to unwind relatively long duplex DNA up to 120-bp and is significantly stimulated by a preexisting fork structure. Further, the most striking feature of Hrq1 is its absolute requirement for a long 3′-tail (⩾70-nt) for efficient unwinding of duplex DNA. We also found that Hrq1 has potent DNA strand annealing activity. Our results indicate that Hrq1 has vigorous helicase activity that deserves further characterization to expand our understanding of RecQ helicases.

  8. Mechanism of Archaeal MCM Helicase Recruitment to DNA Replication Origins

    Science.gov (United States)

    Samson, Rachel Y.; Abeyrathne, Priyanka D.; Bell, Stephen D.

    2015-01-01

    Summary Cellular DNA replication origins direct the recruitment of replicative helicases via the action of initiator proteins belonging to the AAA+ superfamily of ATPases. Archaea have a simplified subset of the eukaryotic DNA replication machinery proteins and possess initiators that appear ancestral to both eukaryotic Orc1 and Cdc6. We have reconstituted origin-dependent recruitment of the homohexameric archaeal MCM in vitro with purified recombinant proteins. Using this system, we reveal that archaeal Orc1-1 fulfills both Orc1 and Cdc6 functions by binding to a replication origin and directly recruiting MCM helicase. We identify the interaction interface between these proteins and reveal how ATP binding by Orc1-1 modulates recruitment of MCM. Additionally, we provide evidence that an open-ring form of the archaeal MCM homohexamer is loaded at origins. PMID:26725007

  9. The MCM Helicase Motor of the Eukaryotic Replisome.

    Science.gov (United States)

    Abid Ali, Ferdos; Costa, Alessandro

    2016-05-08

    The MCM motor of the CMG helicase powers ahead of the eukaryotic replication machinery to unwind DNA, in a process that requires ATP hydrolysis. The reconstitution of DNA replication in vitro has established the succession of events that lead to replication origin activation by the MCM and recent studies have started to elucidate the structural basis of duplex DNA unwinding. Despite the exciting progress, how the MCM translocates on DNA remains a matter of debate. Copyright © 2016. Published by Elsevier Ltd.

  10. Saccharomyces cerevisiae Hrq1 requires a long 3'-tailed DNA substrate for helicase activity.

    Science.gov (United States)

    Kwon, Sung-Hun; Choi, Do-Hee; Lee, Rina; Bae, Sung-Ho

    2012-10-26

    RecQ helicases are well conserved proteins from bacteria to human and function in various DNA metabolism for maintenance of genome stability. Five RecQ helicases are found in humans, whereas only one RecQ helicase has been described in lower eukaryotes. However, recent studies predicted the presence of a second RecQ helicase, Hrq1, in fungal genomes and verified it as a functional gene in fission yeast. Here we show that 3'-5' helicase activity is intrinsically associated with Hrq1 of Saccharomyces cerevisiae. We also determined several biochemical properties of Hrq1 helicase distinguishable from those of other RecQ helicase members. Hrq1 is able to unwind relatively long duplex DNA up to 120-bp and is significantly stimulated by a preexisting fork structure. Further, the most striking feature of Hrq1 is its absolute requirement for a long 3'-tail (⩾70-nt) for efficient unwinding of duplex DNA. We also found that Hrq1 has potent DNA strand annealing activity. Our results indicate that Hrq1 has vigorous helicase activity that deserves further characterization to expand our understanding of RecQ helicases. Copyright © 2012 Elsevier Inc. All rights reserved.

  11. In TFIIH, XPD helicase is exclusively devoted to DNA repair.

    Directory of Open Access Journals (Sweden)

    Jochen Kuper

    2014-09-01

    Full Text Available The eukaryotic XPD helicase is an essential subunit of TFIIH involved in both transcription and nucleotide excision repair (NER. Mutations in human XPD are associated with several inherited diseases such as xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy. We performed a comparative analysis of XPD from Homo sapiens and Chaetomium thermophilum (a closely related thermostable fungal orthologue to decipher the different molecular prerequisites necessary for either transcription or DNA repair. In vitro and in vivo assays demonstrate that mutations in the 4Fe4S cluster domain of XPD abrogate the NER function of TFIIH and do not affect its transcriptional activity. We show that the p44-dependent activation of XPD is promoted by the stimulation of its ATPase activity. Furthermore, we clearly demonstrate that XPD requires DNA binding, ATPase, and helicase activity to function in NER. In contrast, these enzymatic properties are dispensable for transcription initiation. XPD helicase is thus exclusively devoted to NER and merely acts as a structural scaffold to maintain TFIIH integrity during transcription.

  12. Genome-wide identification of SF1 and SF2 helicases from archaea.

    Science.gov (United States)

    Chamieh, Hala; Ibrahim, Hiba; Kozah, Juliana

    2016-01-15

    Archaea microorganisms have long been used as model organisms for the study of protein molecular machines. Archaeal proteins are particularly appealing to study since archaea, even though prokaryotic, possess eukaryotic-like cellular processes. Super Family I (SF1) and Super Family II (SF2) helicase families have been studied in many model organisms, little is known about their presence and distribution in archaea. We performed an exhaustive search of homologs of SF1 and SF2 helicase proteins in 95 complete archaeal genomes. In the present study, we identified the complete sets of SF1 and SF2 helicases in archaea. Comparative analysis between archaea, human and the bacteria E. coli SF1 and SF2 helicases, resulted in the identification of seven helicase families conserved among representatives of the domains of life. This analysis suggests that these helicase families are highly conserved throughout evolution. We highlight the conserved motifs of each family and characteristic domains of the detected families. Distribution of SF1/SF2 families show that Ski2-like, Lhr, Sfth and Rad3-like helicases are ubiquitous among archaeal genomes while the other families are specific to certain archaeal groups. We also report the presence of a novel SF2 helicase specific to archaea domain named Archaea Specific Helicase (ASH). Phylogenetic analysis indicated that ASH has evolved in Euryarchaeota and is evolutionary related to the Ski2-like family with specific characteristic domains. Our study provides the first exhaustive analysis of SF1 and SF2 helicases from archaea. It expands the variety of SF1 and SF2 archaeal helicases known to exist to date and provides a starting point for new biochemical and genetic studies needed to validate their biological functions. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Biological and Molecular Variability of Alfalfa mosaic virus Affecting Alfalfa Crop in Riyadh Region

    Directory of Open Access Journals (Sweden)

    Mohammed A. AL-Saleh

    2013-12-01

    Full Text Available In 2011–2012, sixty nine samples were collected from alfalfa plants showing viral infection symptoms in Riyadh region. Mechanical inoculation with sap prepared from two collected samples out of twenty five possitive for Alfalfa mosaic virus (AMV by ELISA were produced systemic mosaic on Vigna unguiculata and Nicotiana tabacum, local lesion on Chenopodium amaranticolor and C. quinoa. Vicia faba indicator plants that induce mosaic and mottle with AMV-Sagir isolate and no infection with AMV-Wadi aldawasser isolate. Approximately 700-bp was formed by RT-PCR using AMV coat protein specific primer. Samples from infected alfalfa gave positive results, while healthy plant gave negative result using dot blot hybridization assay. The nucleotide sequences of the Saudi isolates were compared with corresponding viral nucleotide sequences reported in GenBank. The obtained results showed that the AMV from Australia, Brazil, Puglia and China had the highest similarity with AMV-Sajer isolate. While, the AMV from Spain and New Zealaland had the lowest similarity with AMV-Sajer and Wadi aldawasser isolates. The data obtained in this study has been deposited in the GenBank under the accession numbers KC434083 and KC434084 for AMV-Sajer and AMV- Wadialdawasser respectively. This is the first report regarding the gnetic make up of AMV in Saudi Arabia.

  14. Removal of phenanthrene in contaminated soil by combination of alfalfa, white-rot fungus, and earthworms.

    Science.gov (United States)

    Deng, Shuguang; Zeng, Defang

    2017-03-01

    The aim of this study was to investigate the removal of phenanthrene by combination of alfalfa, white-rot fungus, and earthworms in soil. A 60-day experiment was conducted. Inoculation with earthworms and/or white-rot fungus increased alfalfa biomass and phenanthrene accumulation in alfalfa. However, inoculations of alfalfa and white-rot fungus can significantly decrease the accumulation of phenanthrene in earthworms. The removal rates for phenanthrene in soil were 33, 48, 66, 74, 85, and 93% under treatments control, only earthworms, only alfalfa, earthworms + alfalfa, alfalfa + white-rot fungus, and alfalfa + earthworms + white-rot fungus, respectively. The present study demonstrated that the combination of alfalfa, earthworms, and white-rot fungus is an effective way to remove phenanthrene in the soil. The removal is mainly via stimulating both microbial development and soil enzyme activity.

  15. Identification of Hydroxyanthraquinones as Novel Inhibitors of Hepatitis C Virus NS3 Helicase

    Science.gov (United States)

    Furuta, Atsushi; Tsubuki, Masayoshi; Endoh, Miduki; Miyamoto, Tatsuki; Tanaka, Junichi; Abdus Salam, Kazi; Akimitsu, Nobuyoshi; Tani, Hidenori; Yamashita, Atsuya; Moriishi, Kohji; Nakakoshi, Masamichi; Sekiguchi, Yuji; Tsuneda, Satoshi; Noda, Naohiro

    2015-01-01

    Hepatitis C virus (HCV) is an important etiological agent of severe liver diseases, including cirrhosis and hepatocellular carcinoma. The HCV genome encodes nonstructural protein 3 (NS3) helicase, which is a potential anti-HCV drug target because its enzymatic activity is essential for viral replication. Some anthracyclines are known to be NS3 helicase inhibitors and have a hydroxyanthraquinone moiety in their structures; mitoxantrone, a hydroxyanthraquinone analogue, is also known to inhibit NS3 helicase. Therefore, we hypothesized that the hydroxyanthraquinone moiety alone could also inhibit NS3 helicase. Here, we performed a structure–activity relationship study on a series of hydroxyanthraquinones by using a fluorescence-based helicase assay. Hydroxyanthraquinones inhibited NS3 helicase with IC50 values in the micromolar range. The inhibitory activity varied depending on the number and position of the phenolic hydroxyl groups, and among different hydroxyanthraquinones examined, 1,4,5,8-tetrahydroxyanthraquinone strongly inhibited NS3 helicase with an IC50 value of 6 µM. Furthermore, hypericin and sennidin A, which both have two hydroxyanthraquinone-like moieties, were found to exert even stronger inhibition with IC50 values of 3 and 0.8 µM, respectively. These results indicate that the hydroxyanthraquinone moiety can inhibit NS3 helicase and suggest that several key chemical structures are important for the inhibition. PMID:26262613

  16. Identification of Hydroxyanthraquinones as Novel Inhibitors of Hepatitis C Virus NS3 Helicase

    Directory of Open Access Journals (Sweden)

    Atsushi Furuta

    2015-08-01

    Full Text Available Hepatitis C virus (HCV is an important etiological agent of severe liver diseases, including cirrhosis and hepatocellular carcinoma. The HCV genome encodes nonstructural protein 3 (NS3 helicase, which is a potential anti-HCV drug target because its enzymatic activity is essential for viral replication. Some anthracyclines are known to be NS3 helicase inhibitors and have a hydroxyanthraquinone moiety in their structures; mitoxantrone, a hydroxyanthraquinone analogue, is also known to inhibit NS3 helicase. Therefore, we hypothesized that the hydroxyanthraquinone moiety alone could also inhibit NS3 helicase. Here, we performed a structure–activity relationship study on a series of hydroxyanthraquinones by using a fluorescence-based helicase assay. Hydroxyanthraquinones inhibited NS3 helicase with IC50 values in the micromolar range. The inhibitory activity varied depending on the number and position of the phenolic hydroxyl groups, and among different hydroxyanthraquinones examined, 1,4,5,8-tetrahydroxyanthraquinone strongly inhibited NS3 helicase with an IC50 value of 6 µM. Furthermore, hypericin and sennidin A, which both have two hydroxyanthraquinone-like moieties, were found to exert even stronger inhibition with IC50 values of 3 and 0.8 µM, respectively. These results indicate that the hydroxyanthraquinone moiety can inhibit NS3 helicase and suggest that several key chemical structures are important for the inhibition.

  17. A role for the fission yeast Rqh1 helicase in chromosome segregation

    DEFF Research Database (Denmark)

    Win, Thein Z; Mankouri, Hocine W; Hickson, Ian D

    2005-01-01

    Schizosaccharomyces pombe Rqh1 protein is a member of the RecQ DNA helicase family. Members of this protein family are mutated in several human genome instability syndromes, including Bloom, Werner and Rothmund-Thomson syndromes. RecQ helicases participate in recombination repair of stalled...

  18. Impurities in alfalfa seed and their impact on processing technology

    OpenAIRE

    Đokić, Dragoslav; Stanisavljević, Rade; Marković, Jordan; Terzić, Dragan; Anđelković, Bojan

    2012-01-01

    The aim of this research was to determine relevant parameters and optimal alfalfa seed processing technology by a comparative analysis of two systems of machinery for processing natural alfalfa seed of different purity (59.0% and 71.0%) and with different content of impurities. The relevant parameters monitored during the test were: pure seed (%), weed seeds and seeds of other crops (%), inert matter (%), amount of processed seed (kg), seed processing time (min), consumption of steel powder (...

  19. Observaciones sobre el Cultivo de la Alfalfa

    Directory of Open Access Journals (Sweden)

    Mejía. Pedro Nel

    1947-09-01

    Full Text Available En 1940, la Secretaría de Agricultura de Caldas estableció en la fracción de la Enea del Municipio de Manizales un pequeño predio experimental o campo de observación para forrajes, destinado al fomento y divulgación de los mismos. Los datos que consignamos en el presente estudio se refiere a los retados experimentales del lote de alfalfa N° 3 de la granja, que está compuesto por una área de 1947 metros cuadrados. Sirve esto para que las personas interesadas hagan la reducción a la plaza (6.400 metros cuadrados y a la hectárea (10.000 metros cuadrados.

  20. Emerging Importance of Helicases in Plant Stress Tolerance: Characterization of Oryza sativa Repair Helicase XPB2 Promoter and Its Functional Validation in Tobacco under Multiple Stresses

    OpenAIRE

    Raikwar, Shailendra; Srivastava, Vineet K.; Gill, Sarvajeet S.; Tuteja, Renu; Tuteja, Narendra

    2015-01-01

    Genetic material always remains at the risk of spontaneous or induced damage which challenges the normal functioning of DNA molecule, thus, DNA repair is vital to protect the organisms against genetic damage. Helicases, the unique molecular motors, are emerged as prospective molecules to engineer stress tolerance in plants and are involved in nucleic acid metabolism including DNA repair. The repair helicase, XPB is an evolutionary conserved protein present in different organisms, including pl...

  1. Emerging importance of helicases in plant stress tolerance: characterization of Oryza sativa repair helicase XPB2 promoter and its functional validation in tobacco under multiple stresses

    OpenAIRE

    Shailendra eRaikwar; Vineet Kumar Shrivastava; Sarvajeet Singh Gill; Renu eTuteja; Narendra eTuteja; Narendra eTuteja

    2015-01-01

    Genetic material always remains at the risk of spontaneous or induced damage which challenges the normal functioning of DNA molecule, thus, DNA repair is vital to protect the organisms against genetic damage. DNA hHelicases, the unique molecular motors, are emerged as potentialprospective molecules to engineer stress tolerance in plants and are involved in a variety of DNA nucleic acid metabolismc processes including DNA repair. The DNA repair helicase, OsXPB2 is an evolutionary conserved pr...

  2. Uncoupling of Protease trans-Cleavage and Helicase Activities in Pestivirus NS3.

    Science.gov (United States)

    Zheng, Fengwei; Lu, Guoliang; Li, Ling; Gong, Peng; Pan, Zishu

    2017-11-01

    The nonstructural protein NS3 from the Flaviviridae family is a multifunctional protein that contains an N-terminal protease and a C-terminal helicase, playing essential roles in viral polyprotein processing and genome replication. Here we report a full-length crystal structure of the classical swine fever virus (CSFV) NS3 in complex with its NS4A protease cofactor segment (PCS) at a 2.35-Å resolution. The structure reveals a previously unidentified ∼2,200-Å 2 intramolecular protease-helicase interface comprising three clusters of interactions, representing a "closed" global conformation related to the NS3-NS4A cis -cleavage event. Although this conformation is incompatible with protease trans -cleavage, it appears to be functionally important and beneficial to the helicase activity, as the mutations designed to perturb this conformation impaired both the helicase activities in vitro and virus production in vivo Our work reveals important features of protease-helicase coordination in pestivirus NS3 and provides a key basis for how different conformational states may explicitly contribute to certain functions of this natural protease-helicase fusion protein. IMPORTANCE Many RNA viruses encode helicases to aid their RNA genome replication and transcription by unwinding structured RNA. Being naturally fused to a protease participating in viral polyprotein processing, the NS3 helicases encoded by the Flaviviridae family viruses are unique. Therefore, how these two enzyme modules coordinate in a single polypeptide is of particular interest. Here we report a previously unidentified conformation of pestivirus NS3 in complex with its NS4A protease cofactor segment (PCS). This conformational state is related to the protease cis -cleavage event and is optimal for the function of helicase. This work provides an important basis to understand how different enzymatic activities of NS3 may be achieved by the coordination between the protease and helicase through different

  3. Comparative structural analysis of human DEAD-box RNA helicases.

    Directory of Open Access Journals (Sweden)

    Patrick Schütz

    2010-09-01

    Full Text Available DEAD-box RNA helicases play various, often critical, roles in all processes where RNAs are involved. Members of this family of proteins are linked to human disease, including cancer and viral infections. DEAD-box proteins contain two conserved domains that both contribute to RNA and ATP binding. Despite recent advances the molecular details of how these enzymes convert chemical energy into RNA remodeling is unknown. We present crystal structures of the isolated DEAD-domains of human DDX2A/eIF4A1, DDX2B/eIF4A2, DDX5, DDX10/DBP4, DDX18/myc-regulated DEAD-box protein, DDX20, DDX47, DDX52/ROK1, and DDX53/CAGE, and of the helicase domains of DDX25 and DDX41. Together with prior knowledge this enables a family-wide comparative structural analysis. We propose a general mechanism for opening of the RNA binding site. This analysis also provides insights into the diversity of DExD/H- proteins, with implications for understanding the functions of individual family members.

  4. The Drosophila Helicase MLE Targets Hairpin Structures in Genomic Transcripts.

    Directory of Open Access Journals (Sweden)

    Simona Cugusi

    2016-01-01

    Full Text Available RNA hairpins are a common type of secondary structures that play a role in every aspect of RNA biochemistry including RNA editing, mRNA stability, localization and translation of transcripts, and in the activation of the RNA interference (RNAi and microRNA (miRNA pathways. Participation in these functions often requires restructuring the RNA molecules by the association of single-strand (ss RNA-binding proteins or by the action of helicases. The Drosophila MLE helicase has long been identified as a member of the MSL complex responsible for dosage compensation. The complex includes one of two long non-coding RNAs and MLE was shown to remodel the roX RNA hairpin structures in order to initiate assembly of the complex. Here we report that this function of MLE may apply to the hairpins present in the primary RNA transcripts that generate the small molecules responsible for RNA interference. Using stocks from the Transgenic RNAi Project and the Vienna Drosophila Research Center, we show that MLE specifically targets hairpin RNAs at their site of transcription. The association of MLE at these sites is independent of sequence and chromosome location. We use two functional assays to test the biological relevance of this association and determine that MLE participates in the RNAi pathway.

  5. Comparative structural analysis of human DEAD-box RNA helicases.

    Science.gov (United States)

    Schütz, Patrick; Karlberg, Tobias; van den Berg, Susanne; Collins, Ruairi; Lehtiö, Lari; Högbom, Martin; Holmberg-Schiavone, Lovisa; Tempel, Wolfram; Park, Hee-Won; Hammarström, Martin; Moche, Martin; Thorsell, Ann-Gerd; Schüler, Herwig

    2010-09-30

    DEAD-box RNA helicases play various, often critical, roles in all processes where RNAs are involved. Members of this family of proteins are linked to human disease, including cancer and viral infections. DEAD-box proteins contain two conserved domains that both contribute to RNA and ATP binding. Despite recent advances the molecular details of how these enzymes convert chemical energy into RNA remodeling is unknown. We present crystal structures of the isolated DEAD-domains of human DDX2A/eIF4A1, DDX2B/eIF4A2, DDX5, DDX10/DBP4, DDX18/myc-regulated DEAD-box protein, DDX20, DDX47, DDX52/ROK1, and DDX53/CAGE, and of the helicase domains of DDX25 and DDX41. Together with prior knowledge this enables a family-wide comparative structural analysis. We propose a general mechanism for opening of the RNA binding site. This analysis also provides insights into the diversity of DExD/H- proteins, with implications for understanding the functions of individual family members.

  6. Molecular Dynamics of the ZIKA Virus NS3 Helicase

    Science.gov (United States)

    Raubenolt, Bryan; Rick, Steven; The Rick Group Team

    The recent outbreaks of the ZIKA virus (ZIKV) and its connection to microcephaly in newborns has raised its awareness as a global threat and many scientific research efforts are currently underway in attempt to create a vaccine. Molecular Dynamics is a powerful method of investigating the physical behavior of protein complexes. ZIKV is comprised of 3 structural and 7 nonstructural proteins. The NS3 helicase protein appears to play a significant role in the replication complex and its inhibition could be a crucial source of antiviral drug design. This research primarily focuses on studying the structural dynamics, over the course of few hundred nanoseconds, of NS3 helicase in the free state, as well as in complex form with human ssRNA, ATP, and an analogue of GTP. RMSD and RMSF plots of each simulation will provide details on the forces involved in the overall stability of the active and inactive states. Furthermore, free energy calculations on a per residue level will reveal the most interactive residues between states and ultimately the primary driving force behind these interactions. Together these analyses will provide highly relevant information on the binding surface chemistry and thus serve as the basis for potential drug design.

  7. Molecular determinants of nucleolar translocation of RNA helicase A

    International Nuclear Information System (INIS)

    Liu Zhe; Kenworthy, Rachael; Green, Christopher; Tang, Hengli

    2007-01-01

    RNA helicase A (RHA) is a member of the DEAH-box family of DNA/RNA helicases involved in multiple cellular processes and the life cycles of many viruses. The subcellular localization of RHA is dynamic despite its steady-state concentration in the nucleoplasm. We have previously shown that it shuttles rapidly between the nucleus and the cytoplasm by virtue of a bidirectional nuclear transport domain (NTD) located in its carboxyl terminus. Here, we investigate the molecular determinants for its translocation within the nucleus and, more specifically, its redistribution from the nucleoplasm to nucleolus or the perinucleolar region. We found that low temperature treatment, transcription inhibition or replication of hepatitis C virus caused the intranuclear redistribution of the protein, suggesting that RHA shuttles between the nucleolus and nucleoplasm and becomes trapped in the nucleolus or the perinucleolar region upon blockade of transport to the nucleoplasm. Both the NTD and ATPase activity were essential for RHA's transport to the nucleolus or perinucleolar region. One of the double-stranded RNA binding domains (dsRBD II) was also required for this nucleolar translocation (NoT) phenotype. RNA interference studies revealed that RHA is essential for survival of cultured hepatoma cells and the ATPase activity appears to be important for this critical role

  8. Complete nucleotide sequence of Alfalfa mosaic virus isolated from alfalfa (Medicago sativa L.) in Argentina.

    Science.gov (United States)

    Trucco, Verónica; de Breuil, Soledad; Bejerman, Nicolás; Lenardon, Sergio; Giolitti, Fabián

    2014-06-01

    The complete nucleotide sequence of an Alfalfa mosaic virus (AMV) isolate infecting alfalfa (Medicago sativa L.) in Argentina, AMV-Arg, was determined. The virus genome has the typical organization described for AMV, and comprises 3,643, 2,593, and 2,038 nucleotides for RNA1, 2 and 3, respectively. The whole genome sequence and each encoding region were compared with those of other four isolates that have been completely sequenced from China, Italy, Spain and USA. The nucleotide identity percentages ranged from 95.9 to 99.1 % for the three RNAs and from 93.7 to 99 % for the protein 1 (P1), protein 2 (P2), movement protein and coat protein (CP) encoding regions, whereas the amino acid identity percentages of these proteins ranged from 93.4 to 99.5 %, the lowest value corresponding to P2. CP sequences of AMV-Arg were compared with those of other 25 available isolates, and the phylogenetic analysis based on the CP gene was carried out. The highest percentage of nucleotide sequence identity of the CP gene was 98.3 % with a Chinese isolate and 98.6 % at the amino acid level with four isolates, two from Italy, one from Brazil and the remaining one from China. The phylogenetic analysis showed that AMV-Arg is closely related to subgroup I of AMV isolates. To our knowledge, this is the first report of a complete nucleotide sequence of AMV from South America and the first worldwide report of complete nucleotide sequence of AMV isolated from alfalfa as natural host.

  9. Detection of new viruses in alfalfa, weeds and cultivated plants growing adjacent to alfalfa fields in Saudi Arabia.

    Science.gov (United States)

    Al-Shahwan, I M; Abdalla, O A; Al-Saleh, M A; Amer, M A

    2017-09-01

    A total of 1368 symptomatic plant samples showing different virus-like symptoms such as mottling, chlorosis, mosaic, yellow mosaic, vein clearing and stunting were collected from alfalfa, weed and cultivated plant species growing in vicinity of alfalfa fields in five principal regions of alfalfa production in Saudi Arabia. DAS-ELISA test indicated occurrence of 11 different viruses in these samples, 10 of which were detected for the first time in Saudi Arabia. Eighty percent of the alfalfa samples and 97.5% of the weed and cultivated plants samples were found to be infected with one or more of these viruses. Nine weed plant species were found to harbor these viruses namely, Sonchus oleraceus, Chenopodium spp., Hibiscus spp., Cichorium intybus , Convolvulus arvensis , Malva parviflora , Rubus fruticosus , Hippuris vulgaris , and Flaveria trinervia . These viruses were also detected in seven cultivated crop plants growing adjacent to the alfalfa fields including Vigna unguiculata , Solanum tuberosum , Solanum melongena , Phaseolus vulgaris , Cucurbita maxima , Capsicum annuum , and Vicia faba . The newly reported viruses together with their respective percent of detection in alfalfa, and in both weeds and cultivated crop plant species together were as follows: Bean leaf roll virus (BLRV) {12.5 and 4.5%}, Lucerne transient streak virus (LTSV) {2.9 and 3.5%}, Bean yellow mosaic virus (BYMV) {1.4 and 4.5%}, Bean common mosaic virus (BCMV) {1.2 and 4.5%}, Red clover vein mosaic virus (RCVMV) {1.2 and 4%}, White clover mosaic virus (WCIMV) {1.0 and 5%}, Cucumber mosaic virus (CMV) {0.8 and 3%}, Pea streak virus (PeSV) {0.4 and 4.5%} and Tobacco streak virus (TSV) {0.3 and 2.5%}. Alfalfa mosaic virus (AMV), the previously reported virus in alfalfa, had the highest percentage of detection in alfalfa accounting for 58.4% and 62.8% in the weeds and cultivated plants. Peanut stunt virus (PSV) was also detected for the first time in Saudi Arabia with a 66.7% of infection in 90

  10. Detection of new viruses in alfalfa, weeds and cultivated plants growing adjacent to alfalfa fields in Saudi Arabia

    Directory of Open Access Journals (Sweden)

    I.M. Al-Shahwan

    2017-09-01

    Full Text Available A total of 1368 symptomatic plant samples showing different virus-like symptoms such as mottling, chlorosis, mosaic, yellow mosaic, vein clearing and stunting were collected from alfalfa, weed and cultivated plant species growing in vicinity of alfalfa fields in five principal regions of alfalfa production in Saudi Arabia. DAS-ELISA test indicated occurrence of 11 different viruses in these samples, 10 of which were detected for the first time in Saudi Arabia. Eighty percent of the alfalfa samples and 97.5% of the weed and cultivated plants samples were found to be infected with one or more of these viruses. Nine weed plant species were found to harbor these viruses namely, Sonchus oleraceus, Chenopodium spp., Hibiscus spp., Cichorium intybus, Convolvulus arvensis, Malva parviflora, Rubus fruticosus, Hippuris vulgaris, and Flaveria trinervia. These viruses were also detected in seven cultivated crop plants growing adjacent to the alfalfa fields including Vigna unguiculata, Solanum tuberosum, Solanum melongena, Phaseolus vulgaris, Cucurbita maxima, Capsicum annuum, and Vicia faba. The newly reported viruses together with their respective percent of detection in alfalfa, and in both weeds and cultivated crop plant species together were as follows: Bean leaf roll virus (BLRV {12.5 and 4.5%}, Lucerne transient streak virus (LTSV {2.9 and 3.5%}, Bean yellow mosaic virus (BYMV {1.4 and 4.5%}, Bean common mosaic virus (BCMV {1.2 and 4.5%}, Red clover vein mosaic virus (RCVMV {1.2 and 4%}, White clover mosaic virus (WCIMV {1.0 and 5%}, Cucumber mosaic virus (CMV {0.8 and 3%}, Pea streak virus (PeSV {0.4 and 4.5%} and Tobacco streak virus (TSV {0.3 and 2.5%}. Alfalfa mosaic virus (AMV, the previously reported virus in alfalfa, had the highest percentage of detection in alfalfa accounting for 58.4% and 62.8% in the weeds and cultivated plants. Peanut stunt virus (PSV was also detected for the first time in Saudi Arabia with a 66.7% of infection in 90

  11. The Use of Gene Modification and Advanced Molecular Structure Analyses towards Improving Alfalfa Forage

    OpenAIRE

    Lei, Yaogeng; Hannoufa, Abdelali; Yu, Peiqiang

    2017-01-01

    Abstract: Alfalfa is one of the most important legume forage crops in the world. In spite of its agronomic and nutritive advantages, alfalfa has some limitations in the usage of pasture forage and hay supplement. High rapid degradation of protein in alfalfa poses a risk of rumen bloat to ruminants which could cause huge economic losses for farmers. Coupled with the relatively high lignin content, which impedes the degradation of carbohydrate in rumen, alfalfa has unbalanced and asynchronous d...

  12. Investigation into the effects of ionizing radiations on growth, development and productivity of alfalfa

    International Nuclear Information System (INIS)

    Mirchev, M.; Antonova, N.

    1974-01-01

    The purpose of this study was to establish optimal doses of gamma radiation for the normal growth and development of alfalfa and for securing the highest possible yields of hay and seed. It is concluded that: presowing irradiation of alfalfa seeds from a Cs 137 source has a beneficial effect on alfalfa growth and development and on the yields of alfalfa hay and seeds; the optimal radiation dose for seeds is 1300 rad; the irradiated seeds retain their germinating power. (E.T.)

  13. PBDE: Structure-Activity Studies for the Inhibition of Hepatitis C Virus NS3 Helicase

    Directory of Open Access Journals (Sweden)

    Kazi Abdus Salam

    2014-04-01

    Full Text Available The helicase portion of the hepatitis C virus nonstructural protein 3 (NS3 is considered one of the most validated targets for developing direct acting antiviral agents. We isolated polybrominated diphenyl ether (PBDE 1 from a marine sponge as an NS3 helicase inhibitor. In this study, we evaluated the inhibitory effects of PBDE (1 on the essential activities of NS3 protein such as RNA helicase, ATPase, and RNA binding activities. The structure-activity relationship analysis of PBDE (1 against the HCV ATPase revealed that the biphenyl ring, bromine, and phenolic hydroxyl group on the benzene backbone might be a basic scaffold for the inhibitory potency.

  14. ATPase activity measurement of DNA replicative helicase from Bacillus stearothermophilus by malachite green method.

    Science.gov (United States)

    Yang, Mu; Wang, Ganggang

    2016-09-15

    The DnaB helicase from Bacillus stearothermophilus (DnaBBst) was a model protein for studying the bacterial DNA replication. In this work, a non-radioactive method for measuring ATPase activity of DnaBBst helicase was described. The working parameters and conditions were optimized. Furthermore, this method was applied to investigate effects of DnaG primase, ssDNA and helicase loader protein (DnaI) on ATPase activity of DnaBBst. Our results showed this method was sensitive and efficient. Moreover, it is suitable for the investigation of functional interaction between DnaB and related factors. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. Do glyphosate resistant feral plants and hay fields spread the transgene to conventional alfalfa seed fields?

    Science.gov (United States)

    In addition to meeting domestic needs, large amounts of alfalfa seed and hay produced in the US are being exported overseas. Because alfalfa is an insect pollinated crop, gene flow is a concern. Adding to this alfalfa readily naturalizes along roadsides, irrigation ditches, and unmanaged habitats; a...

  16. The long-term effects of alfalfa on soil water content in the Loess ...

    African Journals Online (AJOL)

    Administrator

    2011-05-23

    May 23, 2011 ... affect the water content in deep soil and continuous growing alfalfa ... Wasteland, wheat field and six seeded alfalfa (Medicago sativa L.) grasslands with ... The crops (wheat, maize, potato, beans and millet) had been rainfed on all ..... Productivity dynamic of alfalfa and its effects on water eco-environment.

  17. Effects of cutting frequency on alfalfa yield and yield components in ...

    African Journals Online (AJOL)

    Effects of cutting frequency on alfalfa yield and yield components in Songnen Plain, Northeast China. J Chen, F Tang, R Zhu, C Gao, G Di, Y Zhang. Abstract. The productivity and quality of alfalfa (Medicago sativa L.) is strongly influenced by cutting frequency (F). To clarify that the yield and quality of alfalfa if affected by F, ...

  18. 75 FR 1585 - Draft Environmental Impact Statement; Determination of Regulated Status of Alfalfa Genetically...

    Science.gov (United States)

    2010-01-12

    ...] Draft Environmental Impact Statement; Determination of Regulated Status of Alfalfa Genetically... and Forage Genetics International alfalfa lines designated as events J101 and J163 as regulated... International (FGI) alfalfa events J101 and J163 were no longer considered regulated articles under the...

  19. 76 FR 5780 - Determination of Regulated Status of Alfalfa Genetically Engineered for Tolerance to the...

    Science.gov (United States)

    2011-02-02

    ...] Determination of Regulated Status of Alfalfa Genetically Engineered for Tolerance to the Herbicide Glyphosate... decision and determination on the petition regarding the regulated status of alfalfa genetically engineered... regulated status of alfalfa genetically engineered for tolerance to the herbicide glyphosate based on an...

  20. Dynamics of predation on Lygus hesperus (Hemiptera: Miridae) in alfalfa trap cropped organic strawberry

    Science.gov (United States)

    Alfalfa (Medicago sativa L.) can be strategically planted as a trap crop for Lygus spp. in California’s organic strawberry fields. Alfalfa has been shown to attract both Lygus spp. and, in turn, a Lygus-specific parasitoid, Peristenus relictus (Ruthe). However, the impact of alfalfa trap-cropped st...

  1. 75 FR 8299 - Draft Environmental Impact Statement; Determination of Regulated Status of Alfalfa Genetically...

    Science.gov (United States)

    2010-02-24

    ...] Draft Environmental Impact Statement; Determination of Regulated Status of Alfalfa Genetically... making a determination on the status of the Monsanto Company and Forage Genetics International alfalfa... status of the Monsanto Company and Forage Genetics International alfalfa lines designated as events J101...

  2. Over-Expression of Arabidopsis EDT1 Gene Confers Drought Tolerance in Alfalfa (Medicago sativa L.

    Directory of Open Access Journals (Sweden)

    Guangshun Zheng

    2017-12-01

    Full Text Available Alfalfa (Medicago sativa L. is an important legume forage crop with great economic value. However, as the growth of alfalfa is seriously affected by an inadequate supply of water, drought is probably the major abiotic environmental factor that most severely affects alfalfa production worldwide. In an effort to enhance alfalfa drought tolerance, we transformed the Arabidopsis Enhanced Drought Tolerance 1 (AtEDT1 gene into alfalfa via Agrobacterium-mediated transformation. Compared with wild type plants, drought stress treatment resulted in higher survival rates and biomass, but reduced water loss rates in the transgenic plants. Furthermore, transgenic alfalfa plants had increased stomatal size, but reduced stomatal density, and these stomatal changes contributed greatly to reduced water loss from leaves. Importantly, transgenic alfalfa plants exhibited larger root systems with larger root lengths, root weight, and root diameters than wild type plants. The transgenic alfalfa plants had reduced membrane permeability and malondialdehyde content, but higher soluble sugar and proline content, higher superoxide dismutase activity, higher chlorophyll content, enhanced expression of drought-responsive genes, as compared with wild type plants. Notably, transgenic alfalfa plants grew better in a 2-year field trial and showed enhanced growth performance with increased biomass yield. All of our morphological, physiological, and molecular analyses demonstrated that the ectopic expression of AtEDT1 improved growth and enhanced drought tolerance in alfalfa. Our study provides alfalfa germplasm for use in forage improvement programs, and may help to increase alfalfa production in arid lands.

  3. Phytotoxicity of water-soluble substances from alfalfa and barley soil extracts on four crop species.

    Science.gov (United States)

    Read, J J; Jensen, E H

    1989-02-01

    Problems associated with continuously planting alfalfa (Medicago saliva L.) or seeding to thicken depleted alfalfa stands may be due to autotoxicity, an intraspecific form of allelopathy. A bioassay approach was utilized to characterize the specificity and chemical nature of phytotoxins in extracts of alfalfa soils as compared to fallow soil or soil where a cereal was the previous crop. In germination chamber experiments, water-soluble substances present in methanol extracts of soil cropped to alfalfa or barley (Hordeum vulgare L.) decreased seedling root length of alfalfa L-720, winter wheat (Triticum aestivum L. Nugaines) and radish (Raphanus sativa L. Crimson Giant). Five days after germination, seedling dry weights of alfalfa and radish in alfalfa soil extracts were lower compared to wheat or red clover (Trifolium pralense L. Kenland). Growth of red clover was not significantly reduced by soil extracts from cropped soil. Extracts of crop residue screened from soil cropped to alfalfa or barley significantly reduced seedling root length; extracts of alfalfa residue caused a greater inhibition of seedling dry weight than extracts of barely residue. A phytotoxic, unidentified substance present in extracts of crop residue screened from alfalfa soil, which inhibited seedling root length of alfalfa, was isolated by thin-layer chromatography (TLC). Residues from a soil cropped continuously to alfalfa for 10 years had the greatest phytotoxic activity.

  4. Enhancing pollination by attracting & retaining leaf cutting bees (Megachile rotundata) in alfalfa seed production fields

    Science.gov (United States)

    The alfalfa leafcutting bee, Megachile rotundata (F.), has become an important managed pollinator of alfalfa, Medicago sativa L. One problem when using alfalfa leafcutting bees as managed pollinator, is the dispersal of many females upon release, even when adequate nesting sites are present. While d...

  5. Studi tentang pola produksi alfalfa tropis (Medicago sativa L.

    Directory of Open Access Journals (Sweden)

    Rini Dwi Wahyuni

    2012-06-01

    Full Text Available Abstract The research aims to determine the growth pattern of alfalfa in the tropical region, which later can be used as a source of information for the people needed. Research methods used are experimental; the data acquired during the 90 days was showed in a graph and then analyzed using regression analysis with two variables, namely independent variables (cutting age and dependent variables (the nutritive value, height of plants, and production of dry matter (DM, organic matter (OM, and crude protein (CP. The growth pattern of alfalfa in the range 20 to 90 days was quadratic, with the equation of y= -0.0092x2 + 1.6113x – 19.257. At that range of time the alfalfa was still in vegetative growth phase. With increasing age of cutting, the alfalfa chemical compositions of DM and OM increased, but the content of CP decreased.While the production of DM, OM, and CP increased with increasing cutting age. Key words: nutrition, growth, alfalfa, tropics

  6. Gas, Stars, and Star Formation in Alfalfa Dwarf Galaxies

    Science.gov (United States)

    Huang, Shan; Haynes, Martha P.; Giovanelli, Riccardo; Brinchmann, Jarle; Stierwalt, Sabrina; Neff, Susan G.

    2012-01-01

    We examine the global properties of the stellar and Hi components of 229 low H i mass dwarf galaxies extracted from the ALFALFA survey, including a complete sample of 176 galaxies with H i masses ALFALFA dwarfs are faint and of low surface brightness; only 56% of those within the SDSS footprint have a counterpart in the SDSS spectroscopic survey. A large fraction of the dwarfs have high specific star formation rates (SSFRs), and estimates of their SFRs and M* obtained by SED fitting are systematically smaller than ones derived via standard formulae assuming a constant SFR. The increased dispersion of the SSFR distribution at M* approximately less than10(exp 8)M(sub 0) is driven by a set of dwarf galaxies that have low gas fractions and SSFRs; some of these are dE/dSphs in the Virgo Cluster. The imposition of an upper Hi mass limit yields the selection of a sample with lower gas fractions for their M* than found for the overall ALFALFA population. Many of the ALFALFA dwarfs, particularly the Virgo members, have H i depletion timescales shorter than a Hubble time. An examination of the dwarf galaxies within the full ALFALFA population in the context of global star formation (SF) laws is consistent with the general assumptions that gas-rich galaxies have lower SF efficiencies than do optically selected populations and that Hi disks are more extended than stellar ones.

  7. Genetic diversity for fermentable carbohydrates production in alfalfa

    Energy Technology Data Exchange (ETDEWEB)

    Castonguay, Y.; Bertrand, A.; Duceppe, M.O.; Dube, M.P.; Michaud, R. [Agriculture and Agri-Food Canada, Quebec City, PQ (Canada)

    2009-07-01

    Alfalfa has many attributes that renders it suitable for bioethanol production, including its adaptability to diverse environmental conditions without any need for nitrogen fertilizer. However research is needed to develop biofuel-type alfalfa with improved biomass production and standability, increased persistence, and better cell wall degradability. The ethanol conversion rates from alfalfa biomass could be increased by genetically improving the accumulation of readily fermentable non-structural carbohydrates (NSC). This presentation reported on a screening project where genotypes with superior cell wall degradability were identified. NSC accumulation within 300 genotypes was randomly selected within six genetic backgrounds from Europe and North America. Biochemical analyses of dried stems revealed a large genetic variability for NSC content, with concentrations ranging from 20 to 100 mg per g DW. NSC variability was considerably higher in a genetic background of European origin compared to the other populations, therefore emphasizing the potential for genetic improvement for that trait. A modified commercial enzymatic cocktail known as AcceleraseTM 1000 Genencor is being developed to optimize the degradation of alfalfa biomass. DNA extracted from genotypes with the highest and lowest cell wall degradability or NSC accumulation will be pooled and used for bulk segregant analysis of DNA polymorphisms using the PCR-based sequence-related amplified polymorphism technique. It was concluded that the commercial release of biofuel-type alfalfa can be accelerated if the genetic markers associated with these traits can be identified.

  8. A mechanical mechanism for translocation of ring-shaped helicases on DNA and its demonstration in a macroscopic simulation system

    Science.gov (United States)

    Chou, Y. C.

    2018-04-01

    The asymmetry in the two-layered ring structure of helicases and the random thermal fluctuations of the helicase and DNA molecules are considered as the bases for the generation of the force required for translocation of the ring-shaped helicase on DNA. The helicase comprises a channel at its center with two unequal ends, through which strands of DNA can pass. The random collisions between the portion of the DNA strand in the central channel and the wall of the channel generate an impulsive force toward the small end. This impulsive force is the starting point for the helicase to translocate along the DNA with the small end in front. Such a physical mechanism may serve as a complementary for the chemomechanical mechanism of the translocation of helicase on DNA. When the helicase arrives at the junction of ssDNA and dsDNA (a fork), the collision between the helicase and the closest base pair may produce a sufficient impulsive force to break the weak hydrogen bond of the base pair. Thus, the helicase may advance and repeat the process of unwinding the dsDNA strand. This mechanism was tested in a macroscopic simulation system where the helicase was simulated using a truncated-cone structure and DNA was simulated with bead chains. Many features of translocation and unwinding such as translocation on ssDNA and dsDNA, unwinding of dsDNA, rewinding, strand switching, and Holliday junction resolution were reproduced.

  9. Accuracy of genomic selection for alfalfa biomass yield in different reference populations.

    Science.gov (United States)

    Annicchiarico, Paolo; Nazzicari, Nelson; Li, Xuehui; Wei, Yanling; Pecetti, Luciano; Brummer, E Charles

    2015-12-01

    Genomic selection based on genotyping-by-sequencing (GBS) data could accelerate alfalfa yield gains, if it displayed moderate ability to predict parent breeding values. Its interest would be enhanced by predicting ability also for germplasm/reference populations other than those for which it was defined. Predicting accuracy may be influenced by statistical models, SNP calling procedures and missing data imputation strategies. Landrace and variety material from two genetically-contrasting reference populations, i.e., 124 elite genotypes adapted to the Po Valley (sub-continental climate; PV population) and 154 genotypes adapted to Mediterranean-climate environments (Me population), were genotyped by GBS and phenotyped in separate environments for dry matter yield of their dense-planted half-sib progenies. Both populations showed no sub-population genetic structure. Predictive accuracy was higher by joint rather than separate SNP calling for the two data sets, and using random forest imputation of missing data. Highest accuracy was obtained using Support Vector Regression (SVR) for PV, and Ridge Regression BLUP and SVR for Me germplasm. Bayesian methods (Bayes A, Bayes B and Bayesian Lasso) tended to be less accurate. Random Forest Regression was the least accurate model. Accuracy attained about 0.35 for Me in the range of 0.30-0.50 missing data, and 0.32 for PV at 0.50 missing data, using at least 10,000 SNP markers. Cross-population predictions based on a smaller subset of common SNPs implied a relative loss of accuracy of about 25% for Me and 30% for PV. Genome-wide association analyses based on large subsets of M. truncatula-aligned markers revealed many SNPs with modest association with yield, and some genome areas hosting putative QTLs. A comparison of genomic vs. conventional selection for parent breeding value assuming 1-year vs. 5-year selection cycles, respectively, indicated over three-fold greater predicted yield gain per unit time for genomic selection

  10. Multiple centroid method to evaluate the adaptability of alfalfa genotypes

    Directory of Open Access Journals (Sweden)

    Moysés Nascimento

    2015-02-01

    Full Text Available This study aimed to evaluate the efficiency of multiple centroids to study the adaptability of alfalfa genotypes (Medicago sativa L.. In this method, the genotypes are compared with ideotypes defined by the bissegmented regression model, according to the researcher's interest. Thus, genotype classification is carried out as determined by the objective of the researcher and the proposed recommendation strategy. Despite the great potential of the method, it needs to be evaluated under the biological context (with real data. In this context, we used data on the evaluation of dry matter production of 92 alfalfa cultivars, with 20 cuttings, from an experiment in randomized blocks with two repetitions carried out from November 2004 to June 2006. The multiple centroid method proved efficient for classifying alfalfa genotypes. Moreover, it showed no unambiguous indications and provided that ideotypes were defined according to the researcher's interest, facilitating data interpretation.

  11. RTEL1: functions of a disease-associated helicase.

    Science.gov (United States)

    Vannier, Jean-Baptiste; Sarek, Grzegorz; Boulton, Simon J

    2014-07-01

    DNA secondary structures that arise during DNA replication, repair, and recombination (3R) must be processed correctly to prevent genetic instability. Regulator of telomere length 1 (RTEL1) is an essential DNA helicase that disassembles a variety of DNA secondary structures to facilitate 3R processes and to maintain telomere integrity. The past few years have witnessed the emergence of RTEL1 variants that confer increased susceptibility to high-grade glioma, astrocytomas, and glioblastomas. Mutations in RTEL1 have also been implicated in Hoyeraal-Hreidarsson syndrome, a severe form of the bone-marrow failure and cancer predisposition disorder, dyskeratosis congenita. We review these recent findings and highlight its crucial link between DNA secondary-structure metabolism and human disease. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. High-throughput screening assay of hepatitis C virus helicase inhibitors using fluorescence-quenching phenomenon

    International Nuclear Information System (INIS)

    Tani, Hidenori; Akimitsu, Nobuyoshi; Fujita, Osamu; Matsuda, Yasuyoshi; Miyata, Ryo; Tsuneda, Satoshi; Igarashi, Masayuki; Sekiguchi, Yuji; Noda, Naohiro

    2009-01-01

    We have developed a novel high-throughput screening assay of hepatitis C virus (HCV) nonstructural protein 3 (NS3) helicase inhibitors using the fluorescence-quenching phenomenon via photoinduced electron transfer between fluorescent dyes and guanine bases. We prepared double-stranded DNA (dsDNA) with a 5'-fluorescent-dye (BODIPY FL)-labeled strand hybridized with a complementary strand, the 3'-end of which has guanine bases. When dsDNA is unwound by helicase, the dye emits fluorescence owing to its release from the guanine bases. Our results demonstrate that this assay is suitable for quantitative assay of HCV NS3 helicase activity and useful for high-throughput screening for inhibitors. Furthermore, we applied this assay to the screening for NS3 helicase inhibitors from cell extracts of microorganisms, and found several cell extracts containing potential inhibitors.

  13. Crystal structures of the methyltransferase and helicase from the ZIKA 1947 MR766 Uganda strain

    Energy Technology Data Exchange (ETDEWEB)

    Bukrejewska, Malgorzata; Derewenda, Urszula; Radwanska, Malwina; Engel, Daniel A.; Derewenda, Zygmunt S.

    2017-08-15

    Two nonstructural proteins encoded byZika virusstrain MR766 RNA, a methyltransferase and a helicase, were crystallized and their structures were solved and refined at 2.10 and 2.01 Å resolution, respectively. The NS5 methyltransferase contains a boundS-adenosyl-L-methionine (SAM) co-substrate. The NS3 helicase is in the apo form. Comparison with published crystal structures of the helicase in the apo, nucleotide-bound and single-stranded RNA (ssRNA)-bound states suggests that binding of ssRNA to the helicase may occur through conformational selection rather than induced fit.

  14. Molecular detection of a putatively novel cyprinid herpesvirus in sichel (Pelecus cultratus) during a mass mortality event in Hungary.

    Science.gov (United States)

    Doszpoly, Andor; Papp, Melitta; Deákné, Petra P; Glávits, Róbert; Ursu, Krisztina; Dán, Ádám

    2015-05-01

    In the early summer of 2014, mass mortality of sichel (Pelecus cultratus) was observed in Lake Balaton, Hungary. Histological examination revealed degenerative changes within the tubular epithelium, mainly in the distal tubules and collecting ducts in the kidneys and multifocal vacuolisation in the brain stem and cerebellum. Routine molecular investigations showed the presence of the DNA of an unknown alloherpesvirus in some specimens. Subsequently, three genes of the putative herpesviral genome (DNA polymerase, terminase, and helicase) were amplified and partially sequenced. A phylogenetic tree reconstruction based on the concatenated sequence of these three conserved genes implied that the virus belongs to the genus Cyprinivirus within the family Alloherpesviridae. The sequences of the sichel herpesvirus differ markedly from those of the cypriniviruses CyHV-1, CyHV-2 and CyHV-3, putatively representing a fifth species in the genus.

  15. Nucleolin inhibits G4 oligonucleotide unwinding by Werner helicase.

    Directory of Open Access Journals (Sweden)

    Fred E Indig

    Full Text Available The Werner protein (WRNp, a member of the RecQ helicase family, is strongly associated with the nucleolus, as is nucleolin (NCL, an important nucleolar constituent protein. Both WRNp and NCL respond to the effects of DNA damaging agents. Therefore, we have investigated if these nuclear proteins interact and if this interaction has a possible functional significance in DNA damage repair.Here we report that WRNp interacts with the RNA-binding protein, NCL, based on immunoprecipitation, immunofluorescent co-localization in live and fixed cells, and direct binding of purified WRNp to nucleolin. We also map the binding region to the C-terminal domains of both proteins. Furthermore, treatment of U2OS cells with 15 µM of the Topoisomerase I inhibitor, camptothecin, causes the dissociation of the nucleolin-Werner complex in the nucleolus, followed by partial re-association in the nucleoplasm. Other DNA damaging agents, such as hydroxyurea, Mitomycin C, and aphidicolin do not have these effects. Nucleolin or its C-terminal fragment affected the helicase, but not the exonuclease activity of WRNp, by inhibiting WRN unwinding of G4 tetraplex DNA structures, as seen in activity assays and electrophoretic mobility shift assays (EMSA.These data suggest that nucleolin may regulate G4 DNA unwinding by WRNp, possibly in response to certain DNA damaging agents. We postulate that the NCL-WRNp complex may contain an inactive form of WRNp, which is released from the nucleolus upon DNA damage. Then, when required, WRNp is released from inhibition and can participate in the DNA repair processes.

  16. Complete genome sequence of a new enamovirus from Argentina infecting alfalfa plants showing dwarfism symptoms.

    Science.gov (United States)

    Bejerman, Nicolás; Giolitti, Fabián; Trucco, Verónica; de Breuil, Soledad; Dietzgen, Ralf G; Lenardon, Sergio

    2016-07-01

    Alfalfa dwarf disease, probably caused by synergistic interactions of mixed virus infections, is a major and emergent disease that threatens alfalfa production in Argentina. Deep sequencing of diseased alfalfa plant samples from the central region of Argentina resulted in the identification of a new virus genome resembling enamoviruses in sequence and genome structure. Phylogenetic analysis suggests that it is a new member of the genus Enamovirus, family Luteoviridae. The virus is tentatively named "alfalfa enamovirus 1" (AEV-1). The availability of the AEV-1 genome sequence will make it possible to assess the genetic variability of this virus and to construct an infectious clone to investigate its role in alfalfa dwarfism disease.

  17. Ebselen Inhibits Hepatitis C Virus NS3 Helicase Binding to Nucleic Acid and Prevents Viral Replication

    OpenAIRE

    Mukherjee, Sourav; Weiner, Warren S.; Schroeder, Chad E.; Simpson, Denise S.; Hanson, Alicia M.; Sweeney, Noreena L.; Marvin, Rachel K.; Ndjomou, Jean; Kolli, Rajesh; Isailovic, Dragan; Schoenen, Frank J.; Frick, David N.

    2014-01-01

    The hepatitis C virus (HCV) nonstructural protein 3 (NS3) is both a protease, which cleaves viral and host proteins, and a helicase that separates nucleic acid strands, using ATP hydrolysis to fuel the reaction. Many antiviral drugs, and compounds in clinical trials, target the NS3 protease, but few helicase inhibitors that function as antivirals have been reported. This study focuses on the analysis of the mechanism by which ebselen (2-phenyl-1,2-benzisoselenazol-3-one), a compound previousl...

  18. Ebselen inhibits hepatitis C virus NS3 helicase binding to nucleic acid and prevents viral replication.

    Science.gov (United States)

    Mukherjee, Sourav; Weiner, Warren S; Schroeder, Chad E; Simpson, Denise S; Hanson, Alicia M; Sweeney, Noreena L; Marvin, Rachel K; Ndjomou, Jean; Kolli, Rajesh; Isailovic, Dragan; Schoenen, Frank J; Frick, David N

    2014-10-17

    The hepatitis C virus (HCV) nonstructural protein 3 (NS3) is both a protease, which cleaves viral and host proteins, and a helicase that separates nucleic acid strands, using ATP hydrolysis to fuel the reaction. Many antiviral drugs, and compounds in clinical trials, target the NS3 protease, but few helicase inhibitors that function as antivirals have been reported. This study focuses on the analysis of the mechanism by which ebselen (2-phenyl-1,2-benzisoselenazol-3-one), a compound previously shown to be a HCV antiviral agent, inhibits the NS3 helicase. Ebselen inhibited the abilities of NS3 to unwind nucleic acids, to bind nucleic acids, and to hydrolyze ATP, and about 1 μM ebselen was sufficient to inhibit each of these activities by 50%. However, ebselen had no effect on the activity of the NS3 protease, even at 100 times higher ebselen concentrations. At concentrations below 10 μM, the ability of ebselen to inhibit HCV helicase was reversible, but prolonged incubation of HCV helicase with higher ebselen concentrations led to irreversible inhibition and the formation of covalent adducts between ebselen and all 14 cysteines present in HCV helicase. Ebselen analogues with sulfur replacing the selenium were just as potent HCV helicase inhibitors as ebselen, but the length of the linker between the phenyl and benzisoselenazol rings was critical. Modifications of the phenyl ring also affected compound potency over 30-fold, and ebselen was a far more potent helicase inhibitor than other, structurally unrelated, thiol-modifying agents. Ebselen analogues were also more effective antiviral agents, and they were less toxic to hepatocytes than ebselen. Although the above structure-activity relationship studies suggest that ebselen targets a specific site on NS3, we were unable to confirm binding to either the NS3 ATP binding site or nucleic acid binding cleft by examining the effects of ebselen on NS3 proteins lacking key cysteines.

  19. RAPD analysis of alfalfa DNA mutation via N+ implantation

    International Nuclear Information System (INIS)

    Li Yufeng; Huang Qunce; Yu Zengliang; Liang Yunzhang

    2003-01-01

    Germination capacity of alfalfa seeds under low energy N + implantation manifests oscillations going down with dose strength. From analyzing alfalfa genome DNA under low energy N + implantation by RAPD (Random Amplified Polymorphous DNA), it is recommended that 30 polymorphic DNA fragments be amplified with 8 primers in total 100 primers, and fluorescence intensity of the identical DNA fragment amplified by RAPD is different between CK and treatments. Number of different polymorphic DNA fragments between treatment and CK via N + implantation manifests going up with dose strength

  20. Close encounters for the first time: Helicase interactions with DNA damage.

    Science.gov (United States)

    Khan, Irfan; Sommers, Joshua A; Brosh, Robert M

    2015-09-01

    DNA helicases are molecular motors that harness the energy of nucleoside triphosphate hydrolysis to unwinding structured DNA molecules that must be resolved during cellular replication, DNA repair, recombination, and transcription. In vivo, DNA helicases are expected to encounter a wide spectrum of covalent DNA modifications to the sugar phosphate backbone or the nitrogenous bases; these modifications can be induced by endogenous biochemical processes or exposure to environmental agents. The frequency of lesion abundance can vary depending on the lesion type. Certain adducts such as oxidative base modifications can be quite numerous, and their effects can be helix-distorting or subtle perturbations to DNA structure. Helicase encounters with specific DNA lesions and more novel forms of DNA damage will be discussed. We will also review the battery of assays that have been used to characterize helicase-catalyzed unwinding of damaged DNA substrates. Characterization of the effects of specific DNA adducts on unwinding by various DNA repair and replication helicases has proven to be insightful for understanding mechanistic and biological aspects of helicase function in cellular DNA metabolism. Published by Elsevier B.V.

  1. ARCPHdb: A comprehensive protein database for SF1 and SF2 helicase from archaea.

    Science.gov (United States)

    Moukhtar, Mirna; Chaar, Wafi; Abdel-Razzak, Ziad; Khalil, Mohamad; Taha, Samir; Chamieh, Hala

    2017-01-01

    Superfamily 1 and Superfamily 2 helicases, two of the largest helicase protein families, play vital roles in many biological processes including replication, transcription and translation. Study of helicase proteins in the model microorganisms of archaea have largely contributed to the understanding of their function, architecture and assembly. Based on a large phylogenomics approach, we have identified and classified all SF1 and SF2 protein families in ninety five sequenced archaea genomes. Here we developed an online webserver linked to a specialized protein database named ARCPHdb to provide access for SF1 and SF2 helicase families from archaea. ARCPHdb was implemented using MySQL relational database. Web interfaces were developed using Netbeans. Data were stored according to UniProt accession numbers, NCBI Ref Seq ID, PDB IDs and Entrez Databases. A user-friendly interactive web interface has been developed to browse, search and download archaeal helicase protein sequences, their available 3D structure models, and related documentation available in the literature provided by ARCPHdb. The database provides direct links to matching external databases. The ARCPHdb is the first online database to compile all protein information on SF1 and SF2 helicase from archaea in one platform. This database provides essential resource information for all researchers interested in the field. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. XPD Helicase Structures and Activities: Insights into the Cancer and Aging Phenotypes from XPD Mutations

    Energy Technology Data Exchange (ETDEWEB)

    Tainer, John; Fan, Li; Fuss, Jill O.; Cheng, Quen J.; Arvai, Andrew S.; Hammel, Michal; Roberts, Victoria A.; Cooper, Priscilla K.; Tainer, John A.

    2008-06-02

    Mutations in XPD helicase, required for nucleotide excision repair (NER) as part of the transcription/repair complex TFIIH, cause three distinct phenotypes: cancer-prone xeroderma pigmentosum (XP), or aging disorders Cockayne syndrome (CS), and trichothiodystrophy (TTD). To clarify molecular differences underlying these diseases, we determined crystal structures of the XPD catalytic core from Sulfolobus acidocaldarius and measured mutant enzyme activities. Substrate-binding grooves separate adjacent Rad51/RecA-like helicase domains (HD1, HD2) and an arch formed by 4FeS and Arch domains. XP mutations map along the HD1 ATP-binding edge and HD2 DNA-binding channel and impair helicase activity essential for NER. XP/CS mutations both impair helicase activity and likely affect HD2 functional movement. TTD mutants lose or retain helicase activity but map to sites in all four domains expected to cause framework defects impacting TFIIH integrity. These results provide a foundation for understanding disease consequences of mutations in XPD and related 4Fe-4S helicases including FancJ.

  3. XPD Helicase Structures And Activities: Insights Into the Cancer And Aging Phenotypes From XPD Mutations

    Energy Technology Data Exchange (ETDEWEB)

    Fan, L.; Fuss, J.O.; Cheng, Q.J.; Arvai, A.S.; Hammel, M.; Roberts, V.A.; Cooper, P.K.; Tainer, J.A.

    2009-05-18

    Mutations in XPD helicase, required for nucleotide excision repair (NER) as part of the transcription/repair complex TFIIH, cause three distinct phenotypes: cancer-prone xeroderma pigmentosum (XP), or aging disorders Cockayne syndrome (CS), and trichothiodystrophy (TTD). To clarify molecular differences underlying these diseases, we determined crystal structures of the XPD catalytic core from Sulfolobus acidocaldarius and measured mutant enzyme activities. Substrate-binding grooves separate adjacent Rad51/RecA-like helicase domains (HD1, HD2) and an arch formed by 4FeS and Arch domains. XP mutations map along the HD1 ATP-binding edge and HD2 DNA-binding channel and impair helicase activity essential for NER. XP/CS mutations both impair helicase activity and likely affect HD2 functional movement. TTD mutants lose or retain helicase activity but map to sites in all four domains expected to cause framework defects impacting TFIIH integrity. These results provide a foundation for understanding disease consequences of mutations in XPD and related 4Fe-4S helicases including FancJ.

  4. Targeting Dengue Virus NS-3 Helicase by Ligand based Pharmacophore Modeling and Structure based Virtual Screening

    Science.gov (United States)

    Halim, Sobia A.; Khan, Shanza; Khan, Ajmal; Wadood, Abdul; Mabood, Fazal; Hussain, Javid; Al-Harrasi, Ahmed

    2017-10-01

    Dengue fever is an emerging public health concern, with several million viral infections occur annually, for which no effective therapy currently exist. Non-structural protein 3 (NS-3) Helicase encoded by the dengue virus (DENV) is considered as a potential drug target to design new and effective drugs against dengue. Helicase is involved in unwinding of dengue RNA. This study was conducted to design new NS-3 Helicase inhibitor by in silico ligand- and structure based approaches. Initially ligand-based pharmacophore model was generated that was used to screen a set of 1201474 compounds collected from ZINC Database. The compounds matched with the pharmacophore model were docked into the active site of NS-3 helicase. Based on docking scores and binding interactions, twenty five compounds are suggested to be potential inhibitors of NS3 Helicase. The pharmacokinetic properties of these hits were predicted. The selected hits revealed acceptable ADMET properties. This study identified potential inhibitors of NS-3 Helicase in silico, and can be helpful in the treatment of Dengue.

  5. Effects of alfalfa meal on carcase quality and fat metabolism of Muscovy ducks.

    Science.gov (United States)

    Jiang, J F; Song, X M; Huang, X; Wu, J L; Zhou, W D; Zheng, H C; Jiang, Y Q

    2012-01-01

    1. The effects of alfalfa meal on carcase quality and fat metabolism of Muscovy duck were evaluated. The objective of this research was to establish whether alfalfa meal can reduce fat content and improve carcase quality of Muscovy duck. Animal products with a high fat content present a risk factor for many diseases. Reducing fat content in poultry products is an important goal for the poultry industry. 2. A total of 240 14-d-old white Muscovy ducks were selected and randomly allocated to 1 of 4 dietary treatments containing 0, 3, 6, and 9% of alfalfa meal for 5 weeks. Growth performances were recorded and carcase characteristics and lipid parameters were analysed. 3. Results showed that 3, 6, and 9% alfalfa meal in diet had no significant effects on growth performance of Muscovy ducks from 14 to 49 d of age. Ducks given 3, 6, and 9% alfalfa meal had significantly higher dressing percentage and lower abdominal fat percentage compared with those given no alfalfa meal. Ducks given 9% alfalfa meal had higher breast meat percentage compared with those given no alfalfa meal. The concentrations of triglyceride, total cholesterol, low density lipoprotein (LDL), very low density lipoprotein (VLDL) and free fatty acid in serum of ducks fed on alfalfa meal decreased. Alfalfa meal in the diet decreased abdominal fat percentage and improved carcase traits of Muscovy duck. 4. The study showed that dietary alfalfa meal decreased abdominal fat percentage and improved carcase traits, without an adverse effect on performance.

  6. The Use of Gene Modification and Advanced Molecular Structure Analyses towards Improving Alfalfa Forage

    Directory of Open Access Journals (Sweden)

    Yaogeng Lei

    2017-01-01

    Full Text Available Abstract: Alfalfa is one of the most important legume forage crops in the world. In spite of its agronomic and nutritive advantages, alfalfa has some limitations in the usage of pasture forage and hay supplement. High rapid degradation of protein in alfalfa poses a risk of rumen bloat to ruminants which could cause huge economic losses for farmers. Coupled with the relatively high lignin content, which impedes the degradation of carbohydrate in rumen, alfalfa has unbalanced and asynchronous degradation ratio of nitrogen to carbohydrate (N/CHO in rumen. Genetic engineering approaches have been used to manipulate the expression of genes involved in important metabolic pathways for the purpose of improving the nutritive value, forage yield, and the ability to resist abiotic stress. Such gene modification could bring molecular structural changes in alfalfa that are detectable by advanced structural analytical techniques. These structural analyses have been employed in assessing alfalfa forage characteristics, allowing for rapid, convenient and cost-effective analysis of alfalfa forage quality. In this article, we review two major obstacles facing alfalfa utilization, namely poor protein utilization and relatively high lignin content, and highlight genetic studies that were performed to overcome these drawbacks, as well as to introduce other improvements to alfalfa quality. We also review the use of advanced molecular structural analysis in the assessment of alfalfa forage for its potential usage in quality selection in alfalfa breeding.

  7. The Use of Gene Modification and Advanced Molecular Structure Analyses towards Improving Alfalfa Forage.

    Science.gov (United States)

    Lei, Yaogeng; Hannoufa, Abdelali; Yu, Peiqiang

    2017-01-29

    Alfalfa is one of the most important legume forage crops in the world. In spite of its agronomic and nutritive advantages, alfalfa has some limitations in the usage of pasture forage and hay supplement. High rapid degradation of protein in alfalfa poses a risk of rumen bloat to ruminants which could cause huge economic losses for farmers. Coupled with the relatively high lignin content, which impedes the degradation of carbohydrate in rumen, alfalfa has unbalanced and asynchronous degradation ratio of nitrogen to carbohydrate (N/CHO) in rumen. Genetic engineering approaches have been used to manipulate the expression of genes involved in important metabolic pathways for the purpose of improving the nutritive value, forage yield, and the ability to resist abiotic stress. Such gene modification could bring molecular structural changes in alfalfa that are detectable by advanced structural analytical techniques. These structural analyses have been employed in assessing alfalfa forage characteristics, allowing for rapid, convenient and cost-effective analysis of alfalfa forage quality. In this article, we review two major obstacles facing alfalfa utilization, namely poor protein utilization and relatively high lignin content, and highlight genetic studies that were performed to overcome these drawbacks, as well as to introduce other improvements to alfalfa quality. We also review the use of advanced molecular structural analysis in the assessment of alfalfa forage for its potential usage in quality selection in alfalfa breeding.

  8. The Use of Gene Modification and Advanced Molecular Structure Analyses towards Improving Alfalfa Forage

    Energy Technology Data Exchange (ETDEWEB)

    Lei, Yaogeng; Hannoufa, Abdelali; Yu, Peiqiang

    2017-01-29

    Alfalfa is one of the most important legume forage crops in the world. In spite of its agronomic and nutritive advantages, alfalfa has some limitations in the usage of pasture forage and hay supplement. High rapid degradation of protein in alfalfa poses a risk of rumen bloat to ruminants which could cause huge economic losses for farmers. Coupled with the relatively high lignin content, which impedes the degradation of carbohydrate in rumen, alfalfa has unbalanced and asynchronous degradation ratio of nitrogen to carbohydrate (N/CHO) in rumen. Genetic engineering approaches have been used to manipulate the expression of genes involved in important metabolic pathways for the purpose of improving the nutritive value, forage yield, and the ability to resist abiotic stress. Such gene modification could bring molecular structural changes in alfalfa that are detectable by advanced structural analytical techniques. These structural analyses have been employed in assessing alfalfa forage characteristics, allowing for rapid, convenient and cost-effective analysis of alfalfa forage quality. In this article, we review two major obstacles facing alfalfa utilization, namely poor protein utilization and relatively high lignin content, and highlight genetic studies that were performed to overcome these drawbacks, as well as to introduce other improvements to alfalfa quality. We also review the use of advanced molecular structural analysis in the assessment of alfalfa forage for its potential usage in quality selection in alfalfa breeding.

  9. Genome-Wide Association Mapping of Loci Associated with Plant Growth and Forage Production under Salt Stress in Alfalfa (Medicago sativa L.

    Directory of Open Access Journals (Sweden)

    Xiang-Ping Liu

    2017-05-01

    Full Text Available Salinity tolerance is highly desirable to sustain alfalfa production in marginal lands that have been rendered saline. In this study, we used a diverse panel of 198 alfalfa accessions for mapping loci associated with plant growth and forage production under salt stress using genome-wide association studies (GWAS. The plants were genotyped using genotyping-by-sequencing (GBS. A greenhouse procedure was used for phenotyping four agronomic and physiological traits affected by salt stress, including dry weight (DW, plant height (PH, leaf chlorophyll content (LCC, and stomatal conductance (SC. For each trait, a stress susceptibility index (SSI was used to evaluate plant performance under stressed and non-stressed conditions. Marker-trait association identified a total of 42 markers significantly associated with salt tolerance. They were located on all chromosomes except chromosome 2 based on the alignment of their flanking sequences to the reference genome (Medicago truncatula. Of those identified, 13 were associated with multiple traits. Several loci identified in the present study were also identified in previous reports. BLAST search revealed that 19 putative candidate genes linked to 24 significant markers. Among them, B3 DNA-binding protein, Thiaminepyrophosphokinase and IQ calmodulin-binding motif protein were identified among multiple traits in the present and previous studies. With further investigation, these markers and candidates would be useful for developing markers for marker-assisted selection in breeding programs to improve alfalfa cultivars with enhanced tolerance to salt stress.

  10. Rapid analysis of hay attributes using NIRS. Final report, Task II alfalfa supply system

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-10-24

    This final report provides technical information on the development of a near infrared reflectance spectroscopy (NIRS) system for the analysis of alfalfa hay. The purpose of the system is to provide consistent quality for processing alfalfa stems for fuel and alfalfa leaf meal products for livestock feed. Project tasks were to: (1) develop an NIRS driven analytical system for analysis of alfalfa hay and processed alfalfa products; (2) assist in hiring a qualified NIRS technician and recommend changes in testing equipment necessary to provide accurate analysis; (3) calibrate the NIRS instrument for accurate analyses; and (4) develop prototype equipment and sampling procedures as a first step towards development of a totally automated sampling system that would rapidly sample and record incoming feedstock and outbound product. An accurate hay testing program was developed, along with calibration equations for analyzing alfalfa hay and sun-cured alfalfa pellets. A preliminary leaf steam calibration protocol was also developed. 7 refs., 11 figs., 10 tabs.

  11. Occurrence of Transgenic Feral Alfalfa (Medicago sativa subsp. sativa L.) in Alfalfa Seed Production Areas in the United States.

    Science.gov (United States)

    Greene, Stephanie L; Kesoju, Sandya R; Martin, Ruth C; Kramer, Matthew

    2015-01-01

    The potential environmental risks of transgene exposure are not clear for alfalfa (Medicago sativa subsp. sativa), a perennial crop that is cross-pollinated by insects. We gathered data on feral alfalfa in major alfalfa seed-production areas in the western United States to (1) evaluate evidence that feral transgenic plants spread transgenes and (2) determine environmental and agricultural production factors influencing the location of feral alfalfa, especially transgenic plants. Road verges in Fresno, California; Canyon, Idaho; and Walla Walla, Washington were surveyed in 2011 and 2012 for feral plants, and samples were tested for the CP4 EPSPS protein that conveys resistance to glyphosate. Of 4580 sites surveyed, feral plants were observed at 404 sites. Twenty-seven percent of these sites had transgenic plants. The frequency of sites having transgenic feral plants varied among our study areas. Transgenic plants were found in 32.7%, 21.4.7% and 8.3% of feral plant sites in Fresno, Canyon and Walla Walla, respectively. Spatial analysis suggested that feral populations started independently and tended to cluster in seed and hay production areas, places where seed tended to drop. Significant but low spatial auto correlation suggested that in some instances, plants colonized nearby locations. Neighboring feral plants were frequently within pollinator foraging range; however, further research is needed to confirm transgene flow. Locations of feral plant clusters were not well predicted by environmental and production variables. However, the likelihood of seed spillage during production and transport had predictive value in explaining the occurrence of transgenic feral populations. Our study confirms that genetically engineered alfalfa has dispersed into the environment, and suggests that minimizing seed spillage and eradicating feral alfalfa along road sides would be effective strategies to minimize transgene dispersal.

  12. Toxicological responses in alfalfa ( Medicago sativa ) under joint ...

    African Journals Online (AJOL)

    Joint effects of Cd2+ and napropamide in seeds, roots or leaves of alfalfa were investigated under different treatments. It was shown that single stress of Cd2+ or napropamide decreased chlorophyll content after 30 days of treatment in different concentrations. The decrease in chlorophyll content became insignificant under ...

  13. Relationships among alfalfa resistance to Sclerotinia crown and ...

    African Journals Online (AJOL)

    Zilvinas

    2012-09-06

    Sep 6, 2012 ... MATERIALS AND METHODS. Experimental site and plant material. The experiments were carried out at the Institute of Agriculture, during the period of 2009 to 2011. The alfalfa material was subjected for investigation of resistance to S. trifoliorum, OA under laboratory and resistance to SCSR under field ...

  14. Accounting for alfalfa N credits increases returns to corn production

    Science.gov (United States)

    Guidelines are relatively consistent across the Upper Midwest regarding the N benefit of alfalfa to the following grain crops. With higher corn yields and prices, however, some growers have questioned these guidelines and whether more N fertilizer is needed for first-year corn following a good stand...

  15. Thermoperiodism in the cavity nesting alfalfa leafcutting bee, Megachile rotundata

    Science.gov (United States)

    The alfalfa leafcutting bee, Megachile rotundata is the most intensively managed solitary bee, and is the third most used pollinator in the United States. Previous studies have indicated that while the eclosion pattern of this cavity nesting bee is unaffected by photoperiod, a thermoperiod can give...

  16. Modeling of desorption of Alfalfa (Medicago sativa) stems and leaves.

    NARCIS (Netherlands)

    ArabHosseini, A.; Huisman, W.; Müller, J.

    2011-01-01

    The equilibrium moisture content of agricultural products is necessary to optimize drying process and helps to keep the quality of the product during the period of storage. The main aim of this research was to find the best model which could define well, the exchange of moisture between alfalfa

  17. The radiosensitivity of alfalfa varieties and the fuzzy concentration analysis

    International Nuclear Information System (INIS)

    Kang Yufan; Ma Helin

    1994-09-01

    The dried alfalfa seeds (12.1% moisture) were exposed to 6 '0Co γ radiation field with 0∼36.1 C/kg radiation doses (irradiation rate is 2.84 x 10 -2 C/(kg·min)) to observe and measure some radio-bio-effectivity. In the range of irradiation doses, vitality index, root length, seedling survival rate, seedling height, plant height and grass yield decreased and pollen sterility, micro-nucleus rate, free radical relative content increased as the amount of radiation increased. The activity of peroxidase increased as the amount of radiation increased within certain range of dose and tended to decreased beyond that range. Vitality index and root length, which dosage effect curve is compatible with multiple targets-single hit model, and seedling survival rate, seedling height, plant height and grass yield, which dosage effect curve is compatible with linear regression model. There were strong co-relations between the seedling height, micro-nucleus cell rate and the free radical relative content (P<0.01). There were very significant difference (P<0.01) between the alfalfa species and varieties. With fuzzy concentration analysis method, the alfalfa sample were classified into five groups: higher sensitive, sensitive, intermediate, resistant, higher resistant. The suitable irradiation doses for the alfalfa species and varieties are between 12.9∼34.8 mCi/kg

  18. Impact of preceding crop on alfalfa competitiveness with weeds

    Science.gov (United States)

    Organic producers would like to include no-till practices in their farming systems. We are seeking to develop a continuous no-till system for organic farming, based on a complex rotation that includes a 3-year sequence of alfalfa. In this study, we evaluated impact of preceding crop on weed infest...

  19. Photosynthate partitioning and nitrogen fixation of alfalfa and birdsfoot trefoil

    International Nuclear Information System (INIS)

    Shieh, W.J.

    1985-01-01

    Nodule mass and number are usually correlated with rates of nitrogen fixation in legumes. Birdsfoot trefoil (Lotus corniculatus L.) with more than twice the nodule number and mass, however, fixes far less nitrogen than alfalfa (Medicago sativa L.) at the same age. In this research, photosynthesis and photosynthate partitioning and utilization in relation to nitrogen fixation of alfalfa and birdsfoot trefoil were examined in order to determine their relationship to nitrogen fixation potential. Photosynthate to nodules was studied using 14 CO 2 labeling techniques. Partitioning patterns were altered by shading and dark depletion treatments. Efficiency of photosynthate utilization was examined by determining turnover of 14 C photosynthate in nodule metabolites and by studying rates of cyanide-resistant and cyanide-sensitive O 2 uptake. Alfalfa nodule activity was greater than trefoil expressed on a hole pot or nodule dry weight basis. Both shading and dark treatments significantly reduced nodule activity as estimated by the acetylene reduction assay. Shoots of both species were found to be the dominant sinks for photosynthate. Percentage 14 C recovered in alfalfa roots was more than twice that of trefoil at 1,2,3,4 and 24 h after labeling. Greater relative specific radioactivity (RSA) in nodules of both species suggests that they were stronger sinks for current photosynthate than roots

  20. Alfalfa and pastures: sources of pests or generalist natural enemies?

    Science.gov (United States)

    Pierce’s disease of grapevine and almond leaf scorch disease are both caused by the bacterial pathogen Xyllela fastidiosa. In the Central Valley of California, the green sharpshooter is the most common vector of X. fastidiosa. As alfalfa fields and pastures are considered source habitats for green s...

  1. Alfalfa response to irrigation from limited water supplies

    Science.gov (United States)

    A five-year field study (2007-2011) of irrigated alfalfa production with a limited water supply was conducted in southwest Kansas with two years of above-average precipitation, one year of average precipitation, and two years of below-average precipitation. The irrigation treatments were designed to...

  2. Genetic relationships among alfalfa gemplasms resistant to common ...

    African Journals Online (AJOL)

    Genetic relationships among 26 alfalfa cultivars, of which, 12 were of high resistance to common leaf spot (CLS), were assessed using sequence-related amplified polymorphism (SRAP) markers. 34 SRAP primer combinations were selected for fingerprinting of these cultivars and a total of 281 bands were observed, among ...

  3. Managing puncturevine in alfalfa hay and along field edges

    Science.gov (United States)

    Puncturevine (Tribulus terrestris) is a nuisance and difficult to control weed in alfalfa hay field edges and borders. Puncturevine contaminated hay can contain high levels of nitrates and burs can injure mouths of livestock, lowering the value and quality of the hay. Puncturevine is a summer annual...

  4. Genetic relationships among alfalfa gemplasms resistant to common ...

    African Journals Online (AJOL)

    Jane

    2011-10-03

    Oct 3, 2011 ... ... and is the autotetraploid that is naturally outcrossing, and thus is susceptible to inbreeding depression. So, the great majority of alfalfa cultivars are synthetic populations that have been developed from successive generations of random mating of selected. *Corresponding author. E-mail: lxl@caas.net.cn.

  5. Ethanol production from alfalfa fiber fractions by saccharification and fermentation

    Energy Technology Data Exchange (ETDEWEB)

    Sreenath, H.K. [University of Wisconsin, Madison, WI (United States). Dept. of Biological Systems Engineering; USDA Forest Service, Madison, WI (United States). Forest Products Lab.; Koegel, R.G. [US Department of Agriculture, Madison, WI (United States). Dairy Forage Research Center; Moldes, A.B. [USDA Forest Service, Madison, WI (United States). Forest Products Lab.; Universidade de Vigo, Ourense (Spain); Jeffries, T.W. [USDA Forest Service, Madison, WI (United States). Forest Products Lab.; Straub, R.J. [University of Wisconsin, Madison, WI (United States). Dept. of Biological Systems Engineering

    2001-07-01

    This work describes ethanol production from alfalfa fiber using separate hydrolysis and fermentation (SHF) and simultaneous saccharification and fermentation (SSF) with and without liquid hot water (LHW) pretreatment. Candida shehatae FPL-702 produced 5 and 6.4 g/l ethanol with a yield of 0.25 and 0.16 g ethanol/g sugar respectively by SHF and SSF from alfalfa fiber without pretreatment. With LHW pretreatment using SSF, C. shehatae FPL-702 produced 18.0 g/l ethanol, a yield of 0.45 g ethanol/g sugar from cellulosic solids or 'raffinate'. Using SHF, it produced 9.6 g/l ethanol, a yield of 0.47 g ethanol/g sugar from raffinate. However, the soluble extract fraction containing hemicelluloses was poorly fermented in both SHF and SSF due to the presence of inhibitors. Addition of dilute acid during LHW pretreatment of alfalfa fiber resulted in fractions that were poorly saccharified and fermented. These results show that unpretreated alfalfa fiber produced a lower ethanol yield. Although LHW pretreatment can increase ethanol production from raffinate fiber fractions, it does not increase production from the hemicellulosic and pectin fractions. (author)

  6. GAS, STARS, AND STAR FORMATION IN ALFALFA DWARF GALAXIES

    Energy Technology Data Exchange (ETDEWEB)

    Huang Shan; Haynes, Martha P.; Giovanelli, Riccardo [Center for Radiophysics and Space Research, Space Sciences Building, Cornell University, Ithaca, NY 14853 (United States); Brinchmann, Jarle [Sterrewacht Leiden, Leiden University, NL-2300 RA Leiden (Netherlands); Stierwalt, Sabrina [Spitzer Science Center, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125 (United States); Neff, Susan G., E-mail: shan@astro.cornell.edu, E-mail: haynes@astro.cornell.edu, E-mail: riccardo@astro.cornell.edu, E-mail: jarle@strw.leidenuniv.nl, E-mail: sabrina@ipac.caltech.edu, E-mail: susan.g.neff@nasa.gov [NASA GSFC, Code 665, Observational Cosmology Lab, Greenbelt, MD 20771 (United States)

    2012-06-15

    We examine the global properties of the stellar and H I components of 229 low H I mass dwarf galaxies extracted from the ALFALFA survey, including a complete sample of 176 galaxies with H I masses <10{sup 7.7} M{sub Sun} and H I line widths <80 km s{sup -1}. Sloan Digital Sky Survey (SDSS) data are combined with photometric properties derived from Galaxy Evolution Explorer to derive stellar masses (M{sub *}) and star formation rates (SFRs) by fitting their UV-optical spectral energy distributions (SEDs). In optical images, many of the ALFALFA dwarfs are faint and of low surface brightness; only 56% of those within the SDSS footprint have a counterpart in the SDSS spectroscopic survey. A large fraction of the dwarfs have high specific star formation rates (SSFRs), and estimates of their SFRs and M{sub *} obtained by SED fitting are systematically smaller than ones derived via standard formulae assuming a constant SFR. The increased dispersion of the SSFR distribution at M{sub *} {approx}< 10{sup 8} M{sub Sun} is driven by a set of dwarf galaxies that have low gas fractions and SSFRs; some of these are dE/dSphs in the Virgo Cluster. The imposition of an upper H I mass limit yields the selection of a sample with lower gas fractions for their M{sub *} than found for the overall ALFALFA population. Many of the ALFALFA dwarfs, particularly the Virgo members, have H I depletion timescales shorter than a Hubble time. An examination of the dwarf galaxies within the full ALFALFA population in the context of global star formation (SF) laws is consistent with the general assumptions that gas-rich galaxies have lower SF efficiencies than do optically selected populations and that H I disks are more extended than stellar ones.

  7. Environmental impact assessment of alfalfa (Medicago sativa L.) hay production.

    Science.gov (United States)

    Bacenetti, Jacopo; Lovarelli, Daniela; Tedesco, Doriana; Pretolani, Roberto; Ferrante, Valentina

    2018-09-01

    On-farm production of hay and high-protein-content feed has several advantages such as diversification of on-farm cultivated crops, reduction of off-farm feed concentrates transported over long distances and a reduction in runoff during the winter season if grown crops are perennial. Among those crops cultivated for high-protein-content feed, alfalfa (Medicago sativa L.) is one of the most important in the Italian context. Nevertheless, up to now, only a few studies have assessed the environmental performance of alfalfa hay production. In this study, using the Life Cycle Assessment approach, the environmental impact of alfalfa hay production in Northern Italy was analyzed. More in detail, two production practices (without and with irrigation) were compared. The results show that alfalfa hay production in irrigated fields has a better environmental performance compared to non-irrigated production, mainly because of the yield increase achieved with irrigation. In particular, for the Climate Change impact category, the impact is equal to 84.54 and 80.21kgCO 2 /t of hay for the scenario without and with irrigation, respectively. However, for two impact categories (Ozone Depletion and Human Toxicity-No Cancer Effect), the impact of irrigation completely offsets the yield increase, and the cultivation practice without irrigation shows the best environmental performance. For both scenarios, the mechanization of harvest is the main environmental hotspot, mostly due to fuel consumption and related combustion emissions. Wide differences were highlighted by comparing the two scenarios with the Ecoinvent process of alfalfa hay production; these differences are mostly due to the cultivation practice and, in particular, to the more intensive fertilization in Swiss production. Copyright © 2018 Elsevier B.V. All rights reserved.

  8. GAS, STARS, AND STAR FORMATION IN ALFALFA DWARF GALAXIES

    International Nuclear Information System (INIS)

    Huang Shan; Haynes, Martha P.; Giovanelli, Riccardo; Brinchmann, Jarle; Stierwalt, Sabrina; Neff, Susan G.

    2012-01-01

    We examine the global properties of the stellar and H I components of 229 low H I mass dwarf galaxies extracted from the ALFALFA survey, including a complete sample of 176 galaxies with H I masses 7.7 M ☉ and H I line widths –1 . Sloan Digital Sky Survey (SDSS) data are combined with photometric properties derived from Galaxy Evolution Explorer to derive stellar masses (M * ) and star formation rates (SFRs) by fitting their UV-optical spectral energy distributions (SEDs). In optical images, many of the ALFALFA dwarfs are faint and of low surface brightness; only 56% of those within the SDSS footprint have a counterpart in the SDSS spectroscopic survey. A large fraction of the dwarfs have high specific star formation rates (SSFRs), and estimates of their SFRs and M * obtained by SED fitting are systematically smaller than ones derived via standard formulae assuming a constant SFR. The increased dispersion of the SSFR distribution at M * ∼ 8 M ☉ is driven by a set of dwarf galaxies that have low gas fractions and SSFRs; some of these are dE/dSphs in the Virgo Cluster. The imposition of an upper H I mass limit yields the selection of a sample with lower gas fractions for their M * than found for the overall ALFALFA population. Many of the ALFALFA dwarfs, particularly the Virgo members, have H I depletion timescales shorter than a Hubble time. An examination of the dwarf galaxies within the full ALFALFA population in the context of global star formation (SF) laws is consistent with the general assumptions that gas-rich galaxies have lower SF efficiencies than do optically selected populations and that H I disks are more extended than stellar ones.

  9. Physical and functional interactions of Caenorhabditis elegans WRN-1 helicase with RPA-1.

    Science.gov (United States)

    Hyun, Moonjung; Park, Sojin; Kim, Eunsun; Kim, Do-Hyung; Lee, Se-Jin; Koo, Hyeon-Sook; Seo, Yeon-Soo; Ahn, Byungchan

    2012-02-21

    The Caenorhabditis elegans Werner syndrome protein, WRN-1, a member of the RecQ helicase family, has a 3'-5' DNA helicase activity. Worms with defective wrn-1 exhibit premature aging phenotypes and an increased level of genome instability. In response to DNA damage, WRN-1 participates in the initial stages of checkpoint activation in concert with C. elegans replication protein A (RPA-1). WRN-1 helicase is stimulated by RPA-1 on long DNA duplex substrates. However, the mechanism by which RPA-1 stimulates DNA unwinding and the function of the WRN-1-RPA-1 interaction are not clearly understood. We have found that WRN-1 physically interacts with two RPA-1 subunits, CeRPA73 and CeRPA32; however, full-length WRN-1 helicase activity is stimulated by only the CeRPA73 subunit, while the WRN-1(162-1056) fragment that harbors the helicase activity requires both the CeRPA73 and CeRPA32 subunits for the stimulation. We also found that the CeRPA73(1-464) fragment can stimulate WRN-1 helicase activity and that residues 335-464 of CeRPA73 are important for physical interaction with WRN-1. Because CeRPA73 and the CeRPA73(1-464) fragment are able to bind single-stranded DNA (ssDNA), the stimulation of WRN-1 helicase by RPA-1 is most likely due to the ssDNA binding activity of CeRPA73 and the direct interaction of WRN-1 and CeRPA73.

  10. Structure-Based Mutational Analysis of the Hepatitis C Virus NS3 Helicase

    Science.gov (United States)

    Tai, Chun-Ling; Pan, Wen-Ching; Liaw, Shwu-Huey; Yang, Ueng-Cheng; Hwang, Lih-Hwa; Chen, Ding-Shinn

    2001-01-01

    The carboxyl terminus of the hepatitis C virus (HCV) nonstructural protein 3 (NS3) possesses ATP-dependent RNA helicase activity. Based on the conserved sequence motifs and the crystal structures of the helicase domain, 17 mutants of the HCV NS3 helicase were generated. The ATP hydrolysis, RNA binding, and RNA unwinding activities of the mutant proteins were examined in vitro to determine the functional role of the mutated residues. The data revealed that Lys-210 in the Walker A motif and Asp-290, Glu-291, and His-293 in the Walker B motif were crucial to ATPase activity and that Thr-322 and Thr-324 in motif III and Arg-461 in motif VI significantly influenced ATPase activity. When the pairing between His-293 and Gln-460, referred to as gatekeepers, was replaced with the Asp-293/His-460 pair, which makes the NS3 helicase more like the DEAD helicase subgroup, ATPase activity was not restored. It thus indicated that the whole microenvironment surrounding the gatekeepers, rather than the residues per se, was important to the enzymatic activities. Arg-461 and Trp-501 are important residues for RNA binding, while Val-432 may only play a coadjutant role. The data demonstrated that RNA helicase activity was possibly abolished by the loss of ATPase activity or by reduced RNA binding activity. Nevertheless, a low threshold level of ATPase activity was found sufficient for helicase activity. Results in this study provide a valuable reference for efforts under way to develop anti-HCV therapeutic drugs targeting NS3. PMID:11483774

  11. Cdt1 stabilizes an open MCM ring for helicase loading.

    Science.gov (United States)

    Frigola, Jordi; He, Jun; Kinkelin, Kerstin; Pye, Valerie E; Renault, Ludovic; Douglas, Max E; Remus, Dirk; Cherepanov, Peter; Costa, Alessandro; Diffley, John F X

    2017-06-23

    ORC, Cdc6 and Cdt1 act together to load hexameric MCM, the motor of the eukaryotic replicative helicase, into double hexamers at replication origins. Here we show that Cdt1 interacts with MCM subunits Mcm2, 4 and 6, which both destabilizes the Mcm2-5 interface and inhibits MCM ATPase activity. Using X-ray crystallography, we show that Cdt1 contains two winged-helix domains in the C-terminal half of the protein and a catalytically inactive dioxygenase-related N-terminal domain, which is important for MCM loading, but not for subsequent replication. We used these structures together with single-particle electron microscopy to generate three-dimensional models of MCM complexes. These show that Cdt1 stabilizes MCM in a left-handed spiral open at the Mcm2-5 gate. We propose that Cdt1 acts as a brace, holding MCM open for DNA entry and bound to ATP until ORC-Cdc6 triggers ATP hydrolysis by MCM, promoting both Cdt1 ejection and MCM ring closure.

  12. RNases and Helicases in Gram-Positive Bacteria.

    Science.gov (United States)

    Durand, Sylvain; Condon, Ciaran

    2018-04-01

    RNases are key enzymes involved in RNA maturation and degradation. Although they play a crucial role in all domains of life, bacteria, archaea, and eukaryotes have evolved with their own sets of RNases and proteins modulating their activities. In bacteria, these enzymes allow modulation of gene expression to adapt to rapidly changing environments. Today, >20 RNases have been identified in both Escherichia coli and Bacillus subtilis , the paradigms of the Gram-negative and Gram-positive bacteria, respectively. However, only a handful of these enzymes are common to these two organisms and some of them are essential to only one. Moreover, although sets of RNases can be very similar in closely related bacteria such as the Firmicutes Staphylococcus aureus and B. subtilis , the relative importance of individual enzymes in posttranscriptional regulation in these organisms varies. In this review, we detail the role of the main RNases involved in RNA maturation and degradation in Gram-positive bacteria, with an emphasis on the roles of RNase J1, RNase III, and RNase Y. We also discuss how other proteins such as helicases can modulate the RNA-degradation activities of these enzymes.

  13. The C-terminal domain of the Bloom syndrome DNA helicase is essential for genomic stability

    Directory of Open Access Journals (Sweden)

    Noonan James P

    2001-07-01

    Full Text Available Abstract Background Bloom syndrome is a rare cancer-prone disorder in which the cells of affected persons have a high frequency of somatic mutation and genomic instability. Bloom syndrome cells have a distinctive high frequency of sister chromatid exchange and quadriradial formation. BLM, the protein altered in BS, is a member of the RecQ DNA helicase family, whose members share an average of 40% identity in the helicase domain and have divergent N-terminal and C-terminal flanking regions of variable lengths. The BLM DNA helicase has been shown to localize to the ND10 (nuclear domain 10 or PML (promyelocytic leukemia nuclear bodies, where it associates with TOPIIIα, and to the nucleolus. Results This report demonstrates that the N-terminal domain of BLM is responsible for localization of the protein to the nuclear bodies, while the C-terminal domain directs the protein to the nucleolus. Deletions of the N-terminal domain of BLM have little effect on sister chromatid exchange frequency and chromosome stability as compared to helicase and C-terminal mutations which can increase SCE frequency and chromosome abnormalities. Conclusion The helicase activity and the C-terminal domain of BLM are critical for maintaining genomic stability as measured by the sister chromatid exchange assay. The localization of BLM into the nucleolus by the C-terminal domain appears to be more important to genomic stability than localization in the nuclear bodies.

  14. Unzippers, Resolvers and Sensors: A Structural and Functional Biochemistry Tale of RNA Helicases

    Directory of Open Access Journals (Sweden)

    Ana Lúcia Leitão

    2015-01-01

    Full Text Available The centrality of RNA within the biological world is an irrefutable fact that currently attracts increasing attention from the scientific community. The panoply of functional RNAs requires the existence of specific biological caretakers, RNA helicases, devoted to maintain the proper folding of those molecules, resolving unstable structures. However, evolution has taken advantage of the specific position and characteristics of RNA helicases to develop new functions for these proteins, which are at the interface of the basic processes for transference of information from DNA to proteins. RNA helicases are involved in many biologically relevant processes, not only as RNA chaperones, but also as signal transducers, scaffolds of molecular complexes, and regulatory elements. Structural biology studies during the last decade, founded in X-ray crystallography, have characterized in detail several RNA-helicases. This comprehensive review summarizes the structural knowledge accumulated in the last two decades within this family of proteins, with special emphasis on the structure-function relationships of the most widely-studied families of RNA helicases: the DEAD-box, RIG-I-like and viral NS3 classes.

  15. Identification of Alfalfa Leaf Diseases Using Image Recognition Technology.

    Directory of Open Access Journals (Sweden)

    Feng Qin

    Full Text Available Common leaf spot (caused by Pseudopeziza medicaginis, rust (caused by Uromyces striatus, Leptosphaerulina leaf spot (caused by Leptosphaerulina briosiana and Cercospora leaf spot (caused by Cercospora medicaginis are the four common types of alfalfa leaf diseases. Timely and accurate diagnoses of these diseases are critical for disease management, alfalfa quality control and the healthy development of the alfalfa industry. In this study, the identification and diagnosis of the four types of alfalfa leaf diseases were investigated using pattern recognition algorithms based on image-processing technology. A sub-image with one or multiple typical lesions was obtained by artificial cutting from each acquired digital disease image. Then the sub-images were segmented using twelve lesion segmentation methods integrated with clustering algorithms (including K_means clustering, fuzzy C-means clustering and K_median clustering and supervised classification algorithms (including logistic regression analysis, Naive Bayes algorithm, classification and regression tree, and linear discriminant analysis. After a comprehensive comparison, the segmentation method integrating the K_median clustering algorithm and linear discriminant analysis was chosen to obtain lesion images. After the lesion segmentation using this method, a total of 129 texture, color and shape features were extracted from the lesion images. Based on the features selected using three methods (ReliefF, 1R and correlation-based feature selection, disease recognition models were built using three supervised learning methods, including the random forest, support vector machine (SVM and K-nearest neighbor methods. A comparison of the recognition results of the models was conducted. The results showed that when the ReliefF method was used for feature selection, the SVM model built with the most important 45 features (selected from a total of 129 features was the optimal model. For this SVM model, the

  16. Identification of Alfalfa Leaf Diseases Using Image Recognition Technology

    Science.gov (United States)

    Qin, Feng; Liu, Dongxia; Sun, Bingda; Ruan, Liu; Ma, Zhanhong; Wang, Haiguang

    2016-01-01

    Common leaf spot (caused by Pseudopeziza medicaginis), rust (caused by Uromyces striatus), Leptosphaerulina leaf spot (caused by Leptosphaerulina briosiana) and Cercospora leaf spot (caused by Cercospora medicaginis) are the four common types of alfalfa leaf diseases. Timely and accurate diagnoses of these diseases are critical for disease management, alfalfa quality control and the healthy development of the alfalfa industry. In this study, the identification and diagnosis of the four types of alfalfa leaf diseases were investigated using pattern recognition algorithms based on image-processing technology. A sub-image with one or multiple typical lesions was obtained by artificial cutting from each acquired digital disease image. Then the sub-images were segmented using twelve lesion segmentation methods integrated with clustering algorithms (including K_means clustering, fuzzy C-means clustering and K_median clustering) and supervised classification algorithms (including logistic regression analysis, Naive Bayes algorithm, classification and regression tree, and linear discriminant analysis). After a comprehensive comparison, the segmentation method integrating the K_median clustering algorithm and linear discriminant analysis was chosen to obtain lesion images. After the lesion segmentation using this method, a total of 129 texture, color and shape features were extracted from the lesion images. Based on the features selected using three methods (ReliefF, 1R and correlation-based feature selection), disease recognition models were built using three supervised learning methods, including the random forest, support vector machine (SVM) and K-nearest neighbor methods. A comparison of the recognition results of the models was conducted. The results showed that when the ReliefF method was used for feature selection, the SVM model built with the most important 45 features (selected from a total of 129 features) was the optimal model. For this SVM model, the

  17. Demonstration of helicase activity in the nonstructural protein, NSs, of the negative-sense RNA virus, groundnut bud necrosis virus.

    Science.gov (United States)

    Bhushan, Lokesh; Abraham, Ambily; Choudhury, Nirupam Roy; Rana, Vipin Singh; Mukherjee, Sunil Kumar; Savithri, Handanahal Subbarao

    2015-04-01

    The nonstructural protein NSs, encoded by the S RNA of groundnut bud necrosis virus (GBNV) (genus Tospovirus, family Bunyaviridae) has earlier been shown to possess nucleic-acid-stimulated NTPase and 5' α phosphatase activity. ATP hydrolysis is an essential function of a true helicase. Therefore, NSs was tested for DNA helicase activity. The results demonstrated that GBNV NSs possesses bidirectional DNA helicase activity. An alanine mutation in the Walker A motif (K189A rNSs) decreased DNA helicase activity substantially, whereas a mutation in the Walker B motif resulted in a marginal decrease in this activity. The parallel loss of the helicase and ATPase activity in the K189A mutant confirms that NSs acts as a non-canonical DNA helicase. Furthermore, both the wild-type and K189A NSs could function as RNA silencing suppressors, demonstrating that the suppressor activity of NSs is independent of its helicase or ATPase activity. This is the first report of a true helicase from a negative-sense RNA virus.

  18. Detection of Norspermidine and Norspermine in Medicago sativa L. (Alfalfa) 1

    Science.gov (United States)

    Rodriguez-Garay, Benjamin; Phillips, Gregory C.; Kuehn, Glenn D.

    1989-01-01

    Shoot meristem tissues of alfalfa, Medicago sativa L., were found by high performance liquid chromatography analyses to contain the uncommon polyamines, norspermidine and norspermine. The chemical structures of norspermidine and norspermine, purified from alfalfa, were confirmed by comparison of mass spectra with those from authentic standards. The discovery of norspermidine and norspermine in alfalfa implicates the presence of at least two biosynthetic enzymes, a polyamine oxidase and a previously uncharacterized aminopropyltransferase. PMID:16666576

  19. Animal feed compositions containing phytase derived from transgenic alfalfa and methods of use thereof

    Science.gov (United States)

    Austin-Phillips, Sandra; Koegel, Richard G.; Straub, Richard J.; Cook, Mark

    1999-01-01

    A value-added composition of matter containing plant matter from transgenic alfalfa which expresses exogenous phytase activity is disclosed. The phytase activity is a gene product of an exogenous gene encoding for phytase which has been stably incorporated into the genome of alfalfa plants. The transgenic alfalfa expresses phytase activity in nutritionally-significant amounts, thereby enabling its use in animal feeds to eliminate the need for phosphorous supplementation of livestock, poultry, and fish feed rations.

  20. Structural view of the helicase reveals that Zika virus uses a conserved mechanism for unwinding RNA.

    Science.gov (United States)

    Li, Lei; Wang, Jin; Jia, Zhihui; Shaw, Neil

    2018-04-01

    Recent studies suggest a link between infection by Zika virus (ZIKV) and the development of neurological complications. The lack of ZIKV-specific therapeutics has alarmed healthcare professionals worldwide. Here, crystal structures of apo and AMPPNP- and Mn 2+ -bound forms of the essential helicase of ZIKV refined to 1.78 and 1.3 Å resolution, respectively, are reported. The structures reveal a conserved trimodular topology of the helicase. ATP and Mn 2+ are tethered between two RecA-like domains by conserved hydrogen-bonding interactions. The binding of ligands induces the movement of backbone Cα and side-chain atoms. Numerous solvent molecules are observed in the vicinity of the AMPPNP, suggesting a role in catalysis. These high-resolution structures could be useful for the design of inhibitors targeting the helicase of ZIKV for the treatment of infections caused by ZIKV.

  1. Distinct functions of human RecQ helicases during DNA replication.

    Science.gov (United States)

    Urban, Vaclav; Dobrovolna, Jana; Janscak, Pavel

    2017-06-01

    DNA replication is the most vulnerable process of DNA metabolism in proliferating cells and therefore it is tightly controlled and coordinated with processes that maintain genomic stability. Human RecQ helicases are among the most important factors involved in the maintenance of replication fork integrity, especially under conditions of replication stress. RecQ helicases promote recovery of replication forks being stalled due to different replication roadblocks of either exogenous or endogenous source. They prevent generation of aberrant replication fork structures and replication fork collapse, and are involved in proper checkpoint signaling. The essential role of human RecQ helicases in the genome maintenance during DNA replication is underlined by association of defects in their function with cancer predisposition. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Quantitative Simulation of Damage Roots on Inoculated Alfalfa by Arbuscular Mycorrhiza Fungi

    Directory of Open Access Journals (Sweden)

    Ying Liu

    2017-12-01

    Full Text Available Underground mining would cause ground subsidence damage and large amounts of cracks, which would result a loss of surface moisture and nutrient and intensifying drought. There are a few reports about damage to plant roots caused by coal mining. The irregular distribution of plant roots in soil and the different forces generated in process of surface subsidence are difficult to study comprehensively. The technologies to repair damaged plant roots have not been completely perfected yet. Based on quantitative simulation of alfalfa root cut-repair experiment, this paper discusses the influences of inoculated Arbuscular Mycorrhiza Fungi on alfalfa root and the mitigation effects of an inoculation on the growth of alfalfa. Root injured alfalfa were investigated by soil pot experiments. The result indicated that at the same cut degree, the growth situation of inoculated alfalfa is better than the contrast. Compared with the Olsen-P content, at cut level of 0 and 1/3, the sand of inoculated alfalfa has less Olsen-P than contrast, at cut degree of 1/2 and 2/3, the sand of inoculated alfalfa has more Olsen-P than contrast, at degree of 3/4, the sand of inoculated alfalfa has less Olsen-P than contrast, the change trend of Olsen-P content is concerned with the relative strength size of absorb Olsen-P by alfalfa root and dissolve Olsen-P by root exudates and hyphae interstate.

  3. Co-inoculation of arbusculr mycorrhizae and nitrogen fixing bacteria enhance alfalfa yield under saline conditions

    International Nuclear Information System (INIS)

    Zhu, R.; Tang, F.; Liu, F.; Chen, J.

    2016-01-01

    The study was to investigate the effects of combined inoculation of Glomus mosseae (arbusculr mycorrhizae fungi, AMF) and Sinorhizobium meliloti (nitrogen-fixing bacteria, i.e., an Rhizobium meliloti, RM) on yield, nutrient contents, nodulation and mycorrhizal colonization of different alfalfa cultivars under saline conditions. An experiment was conducted to test the efficacy of AMF and RM inoculation in development of salt tolerance in alfalfa cultivars (Zhaodong, Nongjing and Longmu) under different salinity levels (0, 60, 120 and 180 mM NaCl). We found that under non stress condition, double inoculation of alfalfa with rhizobium and AM increased the alfalfa yield, nodule weight and number, as well as shoot proline contents, the most when plants were double inoculated followed by AM and rhizobium inoculation, respectively. Whereas under salinity condition, double inoculation of alfalfa with rhizobium and AM increased alfalfa yield, mycorrhizal infection, nodule weight and number as well as increased in shoot proline content, the most followed by AM and rhizobium inoculation, respectively. The Results suggest that growth of alfalfa may be improved by combined inoculation of alfalfa with AM and rhizobium under salt and non-stress conditions. Alleviation of alfalfa growth under saline condition was perhaps due to an increase in mycorrhizal infection and nodule weight and number as well as an increased in shoot proline content by dual inoculation. (author)

  4. Allelopathic interference of alfalfa (Medicago sativa L.) genotypes to annual ryegrass (Lolium rigidum).

    Science.gov (United States)

    Zubair, Hasan Muhammad; Pratley, James E; Sandral, G A; Humphries, A

    2017-07-01

    Alfalfa (Medicago sativa L.) genotypes at varying densities were investigated for allelopathic impact using annual ryegrass (Lolium rigidum) as the target species in a laboratory bioassay. Three densities (15, 30, and 50 seedlings/beaker) and 40 alfalfa genotypes were evaluated by the equal compartment agar method (ECAM). Alfalfa genotypes displayed a range of allelopathic interference in ryegrass seedlings, reducing root length from 5 to 65%. The growth of ryegrass decreased in response to increasing density of alfalfa seedlings. At the lowest density, Q75 and Titan9 were the least allelopathic genotypes. An overall inhibition index was calculated to rank each alfalfa genotype. Reduction in seed germination of annual ryegrass occurred in the presence of several alfalfa genotypes including Force 10, Haymaster7 and SARDI Five. A comprehensive metabolomic analysis using Quadruple Time of Flight (Q-TOF), was conducted to compare six alfalfa genotypes. Variation in chemical compounds was found between alfalfa root extracts and exudates and also between genotypes. Further individual compound assessments and quantitative study at greater chemical concentrations are needed to clarify the allelopathic activity. Considerable genetic variation exists among alfalfa genotypes for allelopathic activity creating the opportunity for its use in weed suppression through selection.

  5. Evaluation for dinitrogen fixation of alfalfa in field based on δ15N value

    International Nuclear Information System (INIS)

    Yao Yunyin; Chen Ming; Zhang Xizhong

    1992-12-01

    The dinitrogen fixation rate of alfalfa was estimated grown in pot and field experiments. β values (isotope fraction factor) of 7 cultivars of alfalfa (Medicago sativa L.) and white clover (Trifolium repens L.) grown in N-free liquid culture medium were examined. Variations in the δ 15 N values of varieties of alfalfa at growing seasons and forage grasses grown under various conditions were measured. %Ndfa of alfalfa was estimated using the natural 15 N abundance method, 15 N isotope dilution method and total N difference, and their accuracy was compared

  6. Occurrence, Distribution and Properties of Alfalfa Mosaic Virus

    Directory of Open Access Journals (Sweden)

    A.D. Zadjaii

    2002-01-01

    Full Text Available Alfalfa Mosaic Virus (AlflMV was recorded on 21 hosts comprising of four field crops, 14 vegetables, one ornamental plant and two new weed species (Heliotropium europaeum and Ammi majus belonging to nine families. The virus was identified and confirmed on the basis of its biological, serological (ELISA and physical properties. The leaves, stem and crown from systemically infected alfalfa plant contained high concentration of the virus. It was nonpersistently transmitted by cotton aphids (Aphis gossypii. The wide host range, including virus reservoirs, seed-borne infection and insect transmission account for high incidence and distribution of AlfMV in the country. The virus isolate had a dilution end point between 1 x 10-3 to l x 10-4, 65-67 °C thermal inactivation point and a few days in-vitro longevity and appears to be similar to the AlfMV-S strain.

  7. Proteomics analysis of alfalfa response to heat stress.

    Directory of Open Access Journals (Sweden)

    Weimin Li

    Full Text Available The proteome responses to heat stress have not been well understood. In this study, alfalfa (Medicago sativa L. cv. Huaiyin seedlings were exposed to 25 °C (control and 40 °C (heat stress in growth chambers, and leaves were collected at 24, 48 and 72 h after treatment, respectively. The morphological, physiological and proteomic processes were negatively affected under heat stress. Proteins were extracted and separated by two-dimensional polyacrylamide gel electrophoresis (2-DE, and differentially expressed protein spots were identified by mass spectrometry (MS. Totally, 81 differentially expressed proteins were identified successfully by MALDI-TOF/TOF. These proteins were categorized into nine classes: including metabolism, energy, protein synthesis, protein destination/storage, transporters, intracellular traffic, cell structure, signal transduction and disease/defence. Five proteins were further analyzed for mRNA levels. The results of the proteomics analyses provide a better understanding of the molecular basis of heat-stress responses in alfalfa.

  8. DNA binding and unwinding by Hel308 helicase requires dual functions of a winged helix domain.

    Science.gov (United States)

    Northall, Sarah J; Buckley, Ryan; Jones, Nathan; Penedo, J Carlos; Soultanas, Panos; Bolt, Edward L

    2017-09-01

    Hel308 helicases promote genome stability linked to DNA replication in archaea, and have homologues in metazoans. In the crystal structure of archaeal Hel308 bound to a tailed DNA duplex, core helicase domains encircle single-stranded DNA (ssDNA) in a "ratchet" for directional translocation. A winged helix domain (WHD) is also present, but its function is mysterious. We investigated the WHD in full-length Hel308, identifying that mutations in a solvent exposed α-helix resulted in reduced DNA binding and unwinding activities. When isolated from the rest of Hel308, the WHD protein alone bound to duplex DNA but not ssDNA, and DNA binding by WHD protein was abolished by the same mutations as were analyzed in full-length Hel308. Isolated WHD from a human Hel308 homologue (HelQ) also bound to duplex DNA. By disrupting the interface between the Hel308 WHD and a RecA-like domain, a topology typical of Ski2 helicases, we show that this is crucial for ATPase and helicase activities. The data suggest a model in which the WHD promotes activity of Hel308 directly, through binding to duplex DNA that is distinct from ssDNA binding by core helicase, and indirectly through interaction with the RecA-like domain. We propose how the WHD may contribute to ssDNA translocation, resulting in DNA helicase activity or in removal of other DNA bound proteins by "reeling" ssDNA. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Alfalfa Leaf Curl Virus: an Aphid-Transmitted Geminivirus.

    Science.gov (United States)

    Roumagnac, Philippe; Granier, Martine; Bernardo, Pauline; Deshoux, Maëlle; Ferdinand, Romain; Galzi, Serge; Fernandez, Emmanuel; Julian, Charlotte; Abt, Isabelle; Filloux, Denis; Mesléard, François; Varsani, Arvind; Blanc, Stéphane; Martin, Darren P; Peterschmitt, Michel

    2015-09-01

    The family Geminiviridae comprises seven genera differentiated by genome organization, sequence similarity, and insect vector. Capulavirus, an eighth genus, has been proposed to accommodate two newly discovered highly divergent geminiviruses that presently have no known vector. Alfalfa leaf curl virus, identified here as a third capulavirus, is shown to be transmitted by Aphis craccivora. This is the first report of an aphid-transmitted geminivirus. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  10. RNA helicase A is not required for RISC activity.

    Science.gov (United States)

    Liang, Xue-Hai; Crooke, Stanley T

    2013-10-01

    It has been shown that siRNAs can compete with each other or with endogenous miRNAs for RISC components. This competition may complicate the interpretations of phenotypes observed through siRNA-mediated knockdown of genes, especially those genes implicated in the RISC pathway. In this study, we re-examined the function of RNA helicase A (RHA), which has been previously proposed to function in RISC loading based on siRNA-mediated knockdown studies. Here we show that reduced RISC activity or loading of siRNAs was observed only in cells depleted of RHA using siRNA, but not using RNaseH-dependent antisense oligonucleotides (ASOs), suggesting that the impaired RISC function stems from the competition between pre-existing and newly transfected siRNAs, but not from reduction of the RHA protein. This view is further supported by the findings that cells depleted of a control protein, NCL1, using siRNA, but not ASO, exhibited similar defects on the loading and activity of a subsequently transfected siRNA. Transfection of RHA or NCL1 siRNAs, but not ASOs, reduced the levels of endogenous miRNAs, suggesting a competition mechanism. As a positive control, we showed that reduction of MOV10 by either siRNA or ASO decreased siRNA activity, confirming its role in RISC function. Together, our results indicate that RHA is not required for RISC activity or loading, and suggest that proper controls are required when using siRNAs to functionalize genes to avoid competition effects. © 2013. Published by Elsevier B.V. All rights reserved.

  11. Cooperation of DNA-PKcs and WRN helicase in the maintenance of telomeric D-loops

    DEFF Research Database (Denmark)

    Kusumoto-Matsuo, Rika; Opresko, Patricia L; Ramsden, Dale

    2010-01-01

    Werner syndrome is an inherited human progeriod syndrome caused by mutations in the gene encoding the Werner Syndrome protein, WRN. It has both 3'-5' DNA helicase and exonuclease activities, and is suggested to have roles in many aspects of DNA metabolism, including DNA repair and telomere...... D-loop model substrate. In addition, the length of telomeric G-tails decreases in DNA-PKcs knockdown cells, and this phenotype is reversed by overexpression of WRN helicase. These results suggest that WRN and DNA-PKcs may cooperatively prevent G-tail shortening in vivo....

  12. Photosynthate partitioning in alfalfa before harvest and during regrowth

    International Nuclear Information System (INIS)

    Cralle, H.T.; Heichel, G.H.

    1988-01-01

    During the harvest regrowth cycle of alfalfa (Medicago sativa L.) plants, factors such as source to sink distance, sink size, and inter-organ competition continually change. However, consequent changes in the pattern of photosynthate partitioning from leaves to other organs are poorly understood. The authors objective was to examine photosynthate partitioning from upper and lower alfalfa leaves at intervals before herbage harvest and during regrowth after harvest. The uppermost or lowest fully expanded leaf on the longest or dominant stem was labeled with 14 CO 2 . After a 24-h translocation period, the plants were divided into various organs to determine distribution of the radiocarbon. At that time, the upper leaf preferentially partitioned photosynthate to the shoot apex, unexpanded leaves and auxillary shoots of the dominant shoot, whereas the lower leaf preferentially distributed photosynthate to the crown shoots, crown, root, and nodules. Expressions of 14 C partitioning were affected differently by organ mass. While the smallest organs such as nodules and unexpanded leaves always ranked higher for 14 C based on relative specific activity, the largest organs such as roots and crown shoots accumulated the largest percentage of total plant recovered radioactivity. The results illustrate the importance of growth stage and leaf position in photosynthate partitioning in alfalfa and the dominance of herbage meristems for current photosynthate during regrowth

  13. Evaluation of two supplements for the prevention of alfalfa bloat.

    Science.gov (United States)

    Hall, J W; Walker, I; Majak, W

    1994-11-01

    Poloxalene and a mineral mixture feed supplement patented for the treatment of emphysema, polyarthritis, and other pectin related diseases were tested in two trials for their ability to prevent bloat in cattle fed fresh alfalfa. Each trial had a crossover design using three Jersey steers with rumen fistulas per group. Each trial period continued until the total number of cases of bloat reached > or = 24. Treatments were given at 0800 each day. The mineral mixture was given at 100 g/d and 190 mg/kg body weight per day in the first and second trials, respectively. Poloxalene, which was tested only in the second trial, was given at 23 mg/kg body weight per day. Each group of steers was then fed 200 kg of freshly harvested alfalfa in the vegetative to early bloom stages of growth at 0830. In the first trial, only 69% as many cases of bloat occurred on the mineral mixture as on the control treatment, but no significant difference was detected in the second trial. The potency of the alfalfa may have been higher in the second trial, when forage dry matter was lower, magnesium and soluble nitrogen were higher, and bloat occasionally occurred twice a day. Bloat did not occur when the steers were treated with poloxalene. In these trials, poloxalene was completely effective in preventing bloat, but the mineral mixture was only partially so.

  14. Gamma-Ray Doses Affected on Alfalfa (Medicago sativa L.)

    International Nuclear Information System (INIS)

    Zayed, E.M; Tarrad, M.M.; Abd El-Daem, G.A.N.A.

    2013-01-01

    Field experiments were conducted at the experimental from, Nuclear Research Center at Inshas. Atomic Energy Authority (AEA) at Egypt during 2011– 2012 growing seasons on alfalfa genotype. The aim of this investigation to evaluate the effect of different gamma ray doses (100-300 Gy) on the alfalfa yield and related traits. Seeds lots of alfalfa genotype were subjected to five gamma ray treatments (100,150,200,250 and 300 Gray). Over all cuts, the dose treatment 300 Gy increased the majority of studied traits i.e., plant height, No. of shoots/plant, fresh weight/plant, fresh yield/Fadden and dry weight yield/fed. The results observed indicated that. In addition, dose of 200 and 250 Gy increased No. of leaves /plant, No. of shoots/plant, stem diameter and fresh weight /plant. However, the plant dry weight was decreased by all doses used and over all cuts, but the dose of 100 and 150 Gy increased leaves /stem ratio. Meanwhile, the later cuts were more affected by irradiation treatments than the earlier ones. In general, the low doses had negative effects on yield traits, but, the relatively high doses exhibited an increase in yield traits

  15. HI-bearing Ultra Diffuse Galaxies in the ALFALFA Survey

    Science.gov (United States)

    Leisman, Lukas; Janowiecki, Steven; Jones, Michael G.; ALFALFA Almost Darks Team

    2018-01-01

    The Arecibo Legacy Fast ALFA (Arecibo L-band Feed Array) extragalactic HI survey, with over 30,000 high significance extragalactic sources, is well positioned to locate gas-bearing, low surface brightness sources missed by optical detection algorithms. We investigate the nature of a population of HI-bearing sources in ALFALFA with properties similar to "ultra-diffuse" galaxies (UDGs): galaxies with stellar masses of dwarf galaxies, but radii of L* galaxies. These "HI-bearing ultra-diffuse" sources (HUDS) constitute a small, but pertinent, fraction of the dwarf-mass galaxies in ALFALFA. They are bluer and have more irregular morphologies than the optically-selected UDGs found in clusters, and they appear to be gas-rich for their stellar mass, indicating low star formation efficiency. To illuminate potential explanations for the extreme properties of these sources we explore their environments and estimate their halo properties. We conclude that environmental mechanism are unlikely the cause of HUDS' properties, as they exist in environments equivalent to that of the other ALFALFA sources of similar HI-masses, however, we do find some suggestion that these HUDS may reside in high spin parameter halos, a potential explanation for their "ultra-diffuse" nature.

  16. Transcript profiling of two alfalfa genotypes with contrasting cell wall composition in stems using a cross-species platform: optimizing analysis by masking biased probes

    Directory of Open Access Journals (Sweden)

    Jung Hans-Joachim G

    2010-05-01

    Full Text Available Abstract Background The GeneChip® Medicago Genome Array, developed for Medicago truncatula, is a suitable platform for transcript profiling in tetraploid alfalfa [Medicago sativa (L. subsp. sativa]. However, previous research involving cross-species hybridization (CSH has shown that sequence variation between two species can bias transcript profiling by decreasing sensitivity (number of expressed genes detected and the accuracy of measuring fold-differences in gene expression. Results Transcript profiling using the Medicago GeneChip® was conducted with elongating stem (ES and post-elongation stem (PES internodes from alfalfa genotypes 252 and 1283 that differ in stem cell wall concentrations of cellulose and lignin. A protocol was developed that masked probes targeting inter-species variable (ISV regions of alfalfa transcripts. A probe signal intensity threshold was selected that optimized both sensitivity and accuracy. After masking for both ISV regions and previously identified single-feature polymorphisms (SFPs, the number of differentially expressed genes between the two genotypes in both ES and PES internodes was approximately 2-fold greater than the number detected prior to masking. Regulatory genes, including transcription factor and receptor kinase genes that may play a role in development of secondary xylem, were significantly over-represented among genes up-regulated in 252 PES internodes compared to 1283 PES internodes. Several cell wall-related genes were also up-regulated in genotype 252 PES internodes. Real-time quantitative RT-PCR of differentially expressed regulatory and cell wall-related genes demonstrated increased sensitivity and accuracy after masking for both ISV regions and SFPs. Over 1,000 genes that were differentially expressed in ES and PES internodes of genotypes 252 and 1283 were mapped onto putative orthologous loci on M. truncatula chromosomes. Clustering simulation analysis of the differentially expressed genes

  17. The utilization of alfalfa that planted at Tobasa highland, North Sumatra for growing Boerka goat feed

    Directory of Open Access Journals (Sweden)

    Juniar Sirait

    2011-12-01

    Full Text Available Alfalfa (Medicago sativa L. is a herbaceus legume which is potential to be used as goat feed for it’s high production and nutritive value. This research was aimed to study the adaptation of alfalfa planted at highland-moderate climate and it’s utilization for goat feed. This research concists of two activities, ie 1 Agronomy of alfalfa that adapted to highland as a goat feed resource, and 2 The alfalfa usage technology as goat feed. On the first activity alfalfa was planted on highland-moderate climate Gurgur, Tobasa District, North Sumatra Province. Data was collected included: growth percentage, morphology and production aspects, and nutritive value. The harvesting was conducted for three times, where the first cutting had done at 100 days after planting. Investigation of morphology characterirtics was done before alfalfa harvesting. The utilization of alfalfa as goat feed was carried out on the second activity which was arranged in a completely randomized design. Twenty male Boer x Kacang crossbred (Boerka goats of 5-6 months of age with average body weight 14.2±0.8 kg were randomly assigned to four feed treatments where each treatment consited of five replications. The four feed treatments were: P1 = 100% grass + 0% alfalfa; P2 = 90% grass + 10% alfalfa, P3 = 80% grass + 20% alfalfa, and P4 = 70% grass + 30% alfalfa. Data observation included dry matter intake, average daily gain, feed efficiency, and income over feed cost. Results showed that alfalfa growth percentage was 65% with good growth and high either production or nutritive value. The average shoot dry matter production was 438.6 g/m2 which was equivalent to 26.3 t/ha/yr. The crude protein content of alfalfa on the first, second and third harvesting were 17.93; 21.89 and 17.73 per cent, respectively. The utilization of alfalfa that had been processed to be crude-meal can be applied as goat feed. Supplementation of 70% grass and 30% alfalfa meal showed the best results: ADG 59

  18. Variation in alfalfa leafcutting bee, Megachile rotundata, reproductive success according to location of nests in U.S. commercial domiciles

    Science.gov (United States)

    The alfalfa leafcutting bee, Megachile rotundata F., is used extensively to pollinate alfalfa for seed production in western North America. However, it usually is not possible to sustain bee populations in the United States. Variable microenvironments are experienced by developing alfalfa leafcutt...

  19. Alfalfa (Medicago sativa L.) forage production, tissue and soil nutrient concentration under three N based broiler litter regimes

    Science.gov (United States)

    Alfalfa (Medicago sativa L.) is considered as most important forage legume grown in Kentucky. Alfalfa supports many livestock production systems including the beef, dairy, and horse industries in Kentucky. Being a legume, alfalfa typically meets its N requirement through symbiotic N2 fixation, but h...

  20. Development and characterization of the first infectious clone of alfalfa latent virus, a strain of Pea streak virus

    Science.gov (United States)

    Alfalfa (Medicago sativa) is a natural host plant for many plant pathogens including fungi, bacteria, nematodes and viruses. Alfalfa latent virus (ALV) is a member of the carlavirus group and occurs symptomlessly in alfalfa. The first complete genomic sequence of the ALV that was recently obtained i...

  1. Helicase and Polymerase Move Together Close to the Fork Junction and Copy DNA in One-Nucleotide Steps

    Directory of Open Access Journals (Sweden)

    Manjula Pandey

    2014-03-01

    Full Text Available By simultaneously measuring DNA synthesis and dNTP hydrolysis, we show that T7 DNA polymerase and T7 gp4 helicase move in sync during leading-strand synthesis, taking one-nucleotide steps and hydrolyzing one dNTP per base-pair unwound/copied. The cooperative catalysis enables the helicase and polymerase to move at a uniformly fast rate without guanine:cytosine (GC dependency or idling with futile NTP hydrolysis. We show that the helicase and polymerase are located close to the replication fork junction. This architecture enables the polymerase to use its strand-displacement synthesis to increase the unwinding rate, whereas the helicase aids this process by translocating along single-stranded DNA and trapping the unwound bases. Thus, in contrast to the helicase-only unwinding model, our results suggest a model in which the helicase and polymerase are moving in one-nucleotide steps, DNA synthesis drives fork unwinding, and a role of the helicase is to trap the unwound bases and prevent DNA reannealing.

  2. RNA helicase HEL-1 promotes longevity by specifically activating DAF-16/FOXO transcription factor signaling in Caenorhabditis elegans

    Science.gov (United States)

    Seo, Mihwa; Seo, Keunhee; Hwang, Wooseon; Koo, Hee Jung; Hahm, Jeong-Hoon; Yang, Jae-Seong; Han, Seong Kyu; Hwang, Daehee; Kim, Sanguk; Jang, Sung Key; Lee, Yoontae; Nam, Hong Gil; Lee, Seung-Jae V.

    2015-01-01

    The homeostatic maintenance of the genomic DNA is crucial for regulating aging processes. However, the role of RNA homeostasis in aging processes remains unknown. RNA helicases are a large family of enzymes that regulate the biogenesis and homeostasis of RNA. However, the functional significance of RNA helicases in aging has not been explored. Here, we report that a large fraction of RNA helicases regulate the lifespan of Caenorhabditis elegans. In particular, we show that a DEAD-box RNA helicase, helicase 1 (HEL-1), promotes longevity by specifically activating the DAF-16/forkhead box O (FOXO) transcription factor signaling pathway. We find that HEL-1 is required for the longevity conferred by reduced insulin/insulin-like growth factor 1 (IGF-1) signaling (IIS) and is sufficient for extending lifespan. We further show that the expression of HEL-1 in the intestine and neurons contributes to longevity. HEL-1 enhances the induction of a large fraction of DAF-16 target genes. Thus, the RNA helicase HEL-1 appears to promote longevity in response to decreased IIS as a transcription coregulator of DAF-16. Because HEL-1 and IIS are evolutionarily well conserved, a similar mechanism for longevity regulation via an RNA helicase-dependent regulation of FOXO signaling may operate in mammals, including humans. PMID:26195740

  3. A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis

    Directory of Open Access Journals (Sweden)

    Yoko Matsumura

    2016-07-01

    Full Text Available Although the DEAD-box RNA helicase family is ubiquitous in eukaryotes, its developmental role remains unelucidated. Here, we report that cooperative action between the Arabidopsis nucleolar protein RH10, an ortholog of human DEAD-box RNA helicase DDX47, and the epigenetic repressor complex of ASYMMETRIC-LEAVES1 (AS1 and AS2 (AS1-AS2 is critical to repress abaxial (ventral genes ETT/ARF3 and ARF4, which leads to adaxial (dorsal development in leaf primordia at shoot apices. Double mutations of rh10-1 and as2 (or as1 synergistically up-regulated the abaxial genes, which generated abaxialized filamentous leaves with loss of the adaxial domain. DDX47 is part of the small subunit processome (SSUP that mediates rRNA biogenesis. In rh10-1 we found various defects in SSUP-related events, such as: accumulation of 35S/33S rRNA precursors; reduction in the 18S/25S ratio; and nucleolar hypertrophy. Double mutants of as2 with mutations of genes that encode other candidate SSUP-related components such as nucleolin and putative rRNA methyltransferase exhibited similar synergistic defects caused by up-regulation of ETT/ARF3 and ARF4. These results suggest a tight link between putative SSUP and AS1-AS2 in repression of the abaxial-determining genes for cell fate decisions for adaxial development.

  4. A Small Molecule Inhibitor of the BLM Helicase Modulates Chromosome Stability in Human Cells

    DEFF Research Database (Denmark)

    Nguyen, Giang Huong; Dexheimer, Thomas S; Rosenthal, Andrew S

    2013-01-01

    The Bloom's syndrome protein, BLM, is a member of the conserved RecQ helicase family. Although cell lines lacking BLM exist, these exhibit progressive genomic instability that makes distinguishing primary from secondary effects of BLM loss problematic. In order to be able to acutely disable BLM f...

  5. BLM helicase measures DNA unwound before switching strands and hRPA promotes unwinding reinitiation

    Czech Academy of Sciences Publication Activity Database

    Yodh, J.G.; Stevens, B.C.; Kanagaraj, R.; Janščák, Pavel; Ha, T.

    2009-01-01

    Roč. 28, č. 4 (2009), s. 405-416 ISSN 0261-4189 Institutional research plan: CEZ:AV0Z50520514 Keywords : Bloom syndrome * FRET * helicase * hRPA * single molecule Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 8.993, year: 2009

  6. BLM helicase suppresses recombination at G-quadruplex motifs in transcribed genes

    NARCIS (Netherlands)

    van Wietmarschen, Niek; Merzouk, Sarra; Halsema, Nancy; Spierings, Diana C J; Guryev, Victor; Lansdorp, Peter M

    2018-01-01

    Bloom syndrome is a cancer predisposition disorder caused by mutations in the BLM helicase gene. Cells from persons with Bloom syndrome exhibit striking genomic instability characterized by excessive sister chromatid exchange events (SCEs). We applied single-cell DNA template strand sequencing

  7. Human RecQL4 helicase plays critical roles in prostate carcinogenesis

    DEFF Research Database (Denmark)

    Su, Yanrong; Meador, Jarah A; Calaf, Gloria M

    2010-01-01

    Prostate cancer is the second leading cause of cancer-associated deaths among men in the western countries. Here, we report that human RecQL4 helicase, which is implicated in the pathogenesis of a subset of cancer-prone Rothmund-Thomson syndrome, is highly elevated in metastatic prostate cancer c...

  8. The Helicase Activity of Hyperthermophilic Archaeal MCM is Enhanced at High Temperatures by Lysine Methylation.

    Science.gov (United States)

    Xia, Yisui; Niu, Yanling; Cui, Jiamin; Fu, Yang; Chen, Xiaojiang S; Lou, Huiqiang; Cao, Qinhong

    2015-01-01

    Lysine methylation and methyltransferases are widespread in the third domain of life, archaea. Nevertheless, the effects of methylation on archaeal proteins wait to be defined. Here, we report that recombinant sisMCM, an archaeal homolog of Mcm2-7 eukaryotic replicative helicase, is methylated by aKMT4 in vitro. Mono-methylation of these lysine residues occurs coincidently in the endogenous sisMCM protein purified from the hyperthermophilic Sulfolobus islandicus cells as indicated by mass spectra. The helicase activity of mini-chromosome maintenance (MCM) is stimulated by methylation, particularly at temperatures over 70°C. The methylated MCM shows optimal DNA unwinding activity after heat-treatment between 76 and 82°C, which correlates well with the typical growth temperatures of hyperthermophilic Sulfolobus. After methylation, the half life of MCM helicase is dramatically extended at 80°C. The methylated sites are located on the accessible protein surface, which might modulate the intra- and inter- molecular interactions through changing the hydrophobicity and surface charge. Furthermore, the methylation-mimic mutants of MCM show heat resistance helicase activity comparable to the methylated MCM. These data provide the biochemical evidence that posttranslational modifications such as methylation may enhance kinetic stability of proteins under the elevated growth temperatures of hyperthermophilic archaea.

  9. MRE11 complex links RECQ5 helicase to sites of DNA damage

    Czech Academy of Sciences Publication Activity Database

    Zheng, L.; Kanagaraj, R.; Mihaljevic, B.; Schwendener, S.; Sartori, A.A.; Gerrits, B.; Shevelev, Igor; Janščák, Pavel

    2009-01-01

    Roč. 37, č. 8 (2009), s. 2645-2657 ISSN 0305-1048 R&D Projects: GA ČR GA204/09/0565 Institutional research plan: CEZ:AV0Z50520514 Keywords : homologous recombination, * RECQ5 helicase * MRE11 * DNA repair Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 7.479, year: 2009

  10. TFIIH with inactive XPD helicase functions in transcription initiation but is defective in DNA repair

    NARCIS (Netherlands)

    G.S. Winkler (Sebastiaan); U. Fiedler; W. Vermeulen (Wim); F. Coin (Frédéric); R.D. Wood (Richard); H.T.M. Timmers (Marc); G. Weeda (Geert); J.H.J. Hoeijmakers (Jan); S.J. Araú jo; J-M. Egly (Jean-Marc)

    2000-01-01

    textabstractTFIIH is a multisubunit protein complex involved in RNA polymerase II transcription and nucleotide excision repair, which removes a wide variety of DNA lesions including UV-induced photoproducts. Mutations in the DNA-dependent ATPase/helicase subunits of TFIIH, XPB and

  11. FBH1 Helicase Disrupts RAD51 Filaments in Vitro and Modulates Homologous Recombination in Mammalian Cells

    Czech Academy of Sciences Publication Activity Database

    Šimandlová, Jitka; Zagelbaum, J.; Payne, M.J.; Chu, W.K.; Shevelev, Igor; Hanada, K.; Chatterjee, S.; Reid, D.A.; Liu, Y.; Janščák, Pavel; Rothenberg, E.; Hickson, I.D.

    2013-01-01

    Roč. 288, č. 47 (2013), s. 34168-34180 ISSN 0021-9258 R&D Projects: GA ČR GAP305/10/0281 Institutional support: RVO:68378050 Keywords : DNA damage * DNA helicase * DNA recombination * DNA repair * DNA replication Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.600, year: 2013

  12. Interaction between the helicases genetically linked to Fanconi anemia group J and Bloom's syndrome

    DEFF Research Database (Denmark)

    Suhasini, Avvaru N; Rawtani, Nina A; Wu, Yuliang

    2011-01-01

    Bloom's syndrome (BS) and Fanconi anemia (FA) are autosomal recessive disorders characterized by cancer and chromosomal instability. BS and FA group J arise from mutations in the BLM and FANCJ genes, respectively, which encode DNA helicases. In this work, FANCJ and BLM were found to interact...

  13. DNA binding polarity, dimerization, and ATPase ring remodeling in the CMG helicase of the eukaryotic replisome

    Science.gov (United States)

    Costa, Alessandro; Renault, Ludovic; Swuec, Paolo; Petojevic, Tatjana; Pesavento, James J; Ilves, Ivar; MacLellan-Gibson, Kirsty; Fleck, Roland A; Botchan, Michael R; Berger, James M

    2014-01-01

    The Cdc45/Mcm2-7/GINS (CMG) helicase separates DNA strands during replication in eukaryotes. How the CMG is assembled and engages DNA substrates remains unclear. Using electron microscopy, we have determined the structure of the CMG in the presence of ATPγS and a DNA duplex bearing a 3′ single-stranded tail. The structure shows that the MCM subunits of the CMG bind preferentially to single-stranded DNA, establishes the polarity by which DNA enters into the Mcm2-7 pore, and explains how Cdc45 helps prevent DNA from dissociating from the helicase. The Mcm2-7 subcomplex forms a cracked-ring, right-handed spiral when DNA and nucleotide are bound, revealing unexpected congruencies between the CMG and both bacterial DnaB helicases and the AAA+ motor of the eukaryotic proteasome. The existence of a subpopulation of dimeric CMGs establishes the subunit register of Mcm2-7 double hexamers and together with the spiral form highlights how Mcm2-7 transitions through different conformational and assembly states as it matures into a functional helicase. DOI: http://dx.doi.org/10.7554/eLife.03273.001 PMID:25117490

  14. Crystal structure of the FeS cluster-containing nucleotide excision repair helicase XPD.

    Directory of Open Access Journals (Sweden)

    Stefanie C Wolski

    2008-06-01

    Full Text Available DNA damage recognition by the nucleotide excision repair pathway requires an initial step identifying helical distortions in the DNA and a proofreading step verifying the presence of a lesion. This proofreading step is accomplished in eukaryotes by the TFIIH complex. The critical damage recognition component of TFIIH is the XPD protein, a DNA helicase that unwinds DNA and identifies the damage. Here, we describe the crystal structure of an archaeal XPD protein with high sequence identity to the human XPD protein that reveals how the structural helicase framework is combined with additional elements for strand separation and DNA scanning. Two RecA-like helicase domains are complemented by a 4Fe4S cluster domain, which has been implicated in damage recognition, and an alpha-helical domain. The first helicase domain together with the helical and 4Fe4S-cluster-containing domains form a central hole with a diameter sufficient in size to allow passage of a single stranded DNA. Based on our results, we suggest a model of how DNA is bound to the XPD protein, and can rationalize several of the mutations in the human XPD gene that lead to one of three severe diseases, xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy.

  15. Mechanisms of qualitative and quantitative resistance to Aphanomyces root rot in alfalfa

    Science.gov (United States)

    Aphanomyces root rot (ARR), caused by Aphanomyces euteiches, is one of the most important diseases of alfalfa (Medicago sativa) in the United States. Two races of the pathogen are currently recognized. Most modern alfalfa cultivars have high levels of resistance to race 1 but few cultivars have resi...

  16. Effects of alfalfa meal on the intestinal microbial diversity and immunity of growing ducks.

    Science.gov (United States)

    Jiang, J F; Song, X M; Wu, J L; Jiang, Y Q

    2014-12-01

    This study was conducted to investigate the effects of alfalfa meal diets on the intestinal microbial diversity and immunity of growing egg-type ducks. A total of 128 healthy 7-week-old female egg-type Shaoxing ducks were selected and randomly assigned into four dietary treatments: 0%, 3%, 6% and 9% alfalfa meal for 8 weeks. Each treatment consisted of four replicates of eight ducks each. Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) was used to characterize the microbiota. The results showed that the DGGE fingerprints of the V6-V8 fragments of the 16S rRNA from the caeca and faeces of ducks fed 3%, 6% and 9% alfalfa meal had significantly higher microbiota species richness than those fed 0% alfalfa meal (p ducks fed 3%, 6% and 9% alfalfa meal was significantly higher than those fed 0% alfalfa meal (p 0.05), and the 3-9% alfalfa meal did not affect the growth performance of the growing egg-type ducks. The proliferation of T and B lymphocytes was significantly greater (p ducks. Dietary alfalfa meal supplementation increases intestinal microbial community diversity and improves of the immune response growing egg-type ducks. Journal of Animal Physiology and Animal Nutrition © 2014 Blackwell Verlag GmbH.

  17. Roadside alfalfa: Innocent bystanders or conveyers of genetically-engineered traits?

    Science.gov (United States)

    Clumps of alfalfa are a common sight along roads and vacant lots in areas that grow alfalfa for hay or seed. So what role do feral roadside plants play in dispersing transgenes? Is there a risk that transgenic feral plants serve as reservoirs or conduits that might facilitate the movement of transg...

  18. Bacterial stem blight of alfalfa: A disease that increases frost damage

    Science.gov (United States)

    Alfalfa producers count on the first harvest in late spring to deliver the highest tonnage and best quality of forage of the year. A late frost can significantly reduce both yield and quality. Losses are due not only to the physical damage from freezing of the alfalfa stem and leaves but also from d...

  19. First report of race 2 of Colletotrichum trifolii causing anthracnose on alfalfa (Medicago sativa) in Wisconsin

    Science.gov (United States)

    Anthracnose of alfalfa (Medicago sativa), caused by Colletotrichum trifolii, is widespread in the United States. Three physiological races have been described. Race 1 is reported to be the dominant race that is present wherever alfalfa is grown, while race 2 was reported in a limited area in the Mid...

  20. A first report and complete genome sequence of alfalfa enamovirus from Sudan

    Science.gov (United States)

    A full genome sequence of a viral pathogen, provisionally named alfalfa enamovirus 2 (AEV-2), was reconstructed from short reads obtained by Illumina RNA sequencing of alfalfa sample originating from Sudan. Ambiguous nucleotides in the resultant consensus assembly and identity of the predicted virus...

  1. The importance of potassium in resistance to crown rot disease in alfalfa

    Science.gov (United States)

    Nitrogen, phosphate, and potassium (potash, K2O) are the three most important nutrients in alfalfa growth and development. Nitrogen fertilization is not required because alfalfa has a high rate of biological nitrogen fixation. Phosphorus and potassium are frequently applied as fertilizer, but potass...

  2. Forage accumulation and nutritive value of reduced lignin and reference alfalfa cultivars

    Science.gov (United States)

    Reduced lignin alfalfa (Medicago sativa L.) cultivars have the potential to increase the feeding value of alfalfa for livestock by improving the forage fiber digestibility and to increase harvest management flexibility. The objectives were to compare the yield and forage nutritive value of reduced ...

  3. Chloroxyanion residue on seeds and sprouts after chlorine dioxide sanitation of alfalfa seed

    Science.gov (United States)

    The effects of a 6-h chlorine dioxide sanitation of alfalfa seed (0, 50, 100, and 200 mg/kg seed) on total coliform bacteria, seed germination, and on the presence of chlorate and perchlorate residues in seed rinse, seed soak, and in alfalfa sprouts was determined. Chlorate residues in 20000 ppm cal...

  4. Advances in improvement of stress tolerance by induced mutation and genetic transformation in alfalfa

    International Nuclear Information System (INIS)

    Huang Xin; Ye Hongxia; Shu Xiaoli; Wu Dianxing

    2008-01-01

    In order to provide references for stress-tolerant breeding of alfalfa, genetic basis of stress-tolerant traits was briefly introduced and advanced in improvement of stress-tolerance by induced mutation and genetic transformation in alfalfa were reviewed. (authors)

  5. VizieR Online Data Catalog: HI-bearing ultra-diffuse ALFALFA galaxies (Leisman+, 2017)

    Science.gov (United States)

    Leisman, L.; Haynes, M. P.; Janowiecki, S.; Hallenbeck, G.; Jozsa, G.; Giovanelli, R.; Adams, E. A. K.; Neira, D. B.; Cannon, J. M.; Janesh, W. F.; Rhode, K. L.; Salzer, J. J.

    2018-02-01

    All sources discussed here have available SDSS and ALFALFA data. The ALFALFA observations, data reduction, and catalog products are detailed elsewhere (e.g., Giovanelli+ 2005AJ....130.2598G ; Saintonge 2007AJ....133.2087S ; Haynes+ 2011, J/AJ/142/170). (1 data file).

  6. First report of Fusarium wilt of alfalfa caused by Fusarium oxysporum f. sp. medicaginis in Wisconsin

    Science.gov (United States)

    Fusarium wilt, caused by Fusarium oxysporum f. sp. medicaginis, is an economically important vascular disease of alfalfa (Medicago sativa) throughout the world. Alfalfa plants with foliar wilt symptoms and reddish-brown arcs in roots consistent with Fusarium wilt were observed in disease assessment ...

  7. Effects of different corn silage: Alfalfa silage ratios and full fat ...

    African Journals Online (AJOL)

    Full fat extruded soybeans addition increased the ether extract in diets and content of conjugated linoleic acids in milk, but it had no effect on fat, protein and lactose content in milk. Milk fat and lactose were not affected by replacing corn silage with alfalfa silage in diets. Increasing alfalfa silage content in the diets increased ...

  8. Interaction of bale size and preservative rate for large-round bales of alfalfa hay

    Science.gov (United States)

    Recently, two studies conducted at the US Dairy Forage Research Center have reported inconsistent storage responses following the application of propionic-acid-based preservatives to alfalfa or alfalfa-orchardgrass hays. One of these studies utilized 5-foot-diameter round bales, and produced disappo...

  9. Alfalfa transgene dispersal and adventitious presence: understanding grower perception of risk

    Science.gov (United States)

    Recognizing the importance of coexistence, the alfalfa industry has developed a set of Best Management Practices (BMP) to maintain separation of GE and conventional production. But the success of BMP depends upon the degree that growers comply. Therefore we surveyed 530 alfalfa hay and seed producer...

  10. Archaeal orthologs of Cdc45 and GINS form a stable complex that stimulates the helicase activity of MCM.

    Science.gov (United States)

    Xu, Yuli; Gristwood, Tamzin; Hodgson, Ben; Trinidad, Jonathan C; Albers, Sonja-Verena; Bell, Stephen D

    2016-11-22

    The regulated recruitment of Cdc45 and GINS is key to activating the eukaryotic MCM(2-7) replicative helicase. We demonstrate that the homohexameric archaeal MCM helicase associates with orthologs of GINS and Cdc45 in vivo and in vitro. Association of these factors with MCM robustly stimulates the MCM helicase activity. In contrast to the situation in eukaryotes, archaeal Cdc45 and GINS form an extremely stable complex before binding MCM. Further, the archaeal GINS•Cdc45 complex contains two copies of Cdc45. Our analyses give insight into the function and evolution of the conserved core of the archaeal/eukaryotic replisome.

  11. The effect of ion-implantation on germination of alfalfa under phenanthrene stress

    International Nuclear Information System (INIS)

    Huang Hong; Wang Naiyan; Huang Jianwei; Liu Xijian; Dou Junfeng; Du Yongchao; Li Shuairan

    2011-01-01

    To investigate mutagenic effects of polycyclic aromatic hydrocarbons (PAHs) degradation plant under phenanthrene stress and to test germination level of alfalfa after ion-implantation alfalfa seeds were irradiated with N + beam. The germination percentage and the root length distribution of alfalfa, which grew in environment with different mass fraction of phenanthrene was investigated, respectively. The results indicated that the relation of dose and germination rate was shown as 'saddle' curve characteristics. It was found that the 5 x 10 15 cm -2 would be the best dose of implantation. And the longest root length was about 10.32 cm. The experiment also showed phenanthrene would have inhibitive effect on germination percentage and root growth of alfalfa. The stress resistance of PAHs with alfalfa could be enhanced by ion implantation. (authors)

  12. Enzymatic activities and DNA substrate specificity of Mycobacterium tuberculosis DNA helicase XPB.

    Science.gov (United States)

    Balasingham, Seetha V; Zegeye, Ephrem Debebe; Homberset, Håvard; Rossi, Marie L; Laerdahl, Jon K; Bohr, Vilhelm A; Tønjum, Tone

    2012-01-01

    XPB, also known as ERCC3 and RAD25, is a 3' → 5' DNA repair helicase belonging to the superfamily 2 of helicases. XPB is an essential core subunit of the eukaryotic basal transcription factor complex TFIIH. It has two well-established functions: in the context of damaged DNA, XPB facilitates nucleotide excision repair by unwinding double stranded DNA (dsDNA) surrounding a DNA lesion; while in the context of actively transcribing genes, XPB facilitates initiation of RNA polymerase II transcription at gene promoters. Human and other eukaryotic XPB homologs are relatively well characterized compared to conserved homologs found in mycobacteria and archaea. However, more insight into the function of bacterial helicases is central to understanding the mechanism of DNA metabolism and pathogenesis in general. Here, we characterized Mycobacterium tuberculosis XPB (Mtb XPB), a 3'→5' DNA helicase with DNA-dependent ATPase activity. Mtb XPB efficiently catalyzed DNA unwinding in the presence of significant excess of enzyme. The unwinding activity was fueled by ATP or dATP in the presence of Mg(2+)/Mn(2+). Consistent with the 3'→5' polarity of this bacterial XPB helicase, the enzyme required a DNA substrate with a 3' overhang of 15 nucleotides or more. Although Mtb XPB efficiently unwound DNA model substrates with a 3' DNA tail, it was not active on substrates containing a 3' RNA tail. We also found that Mtb XPB efficiently catalyzed ATP-independent annealing of complementary DNA strands. These observations significantly enhance our understanding of the biological roles of Mtb XPB.

  13. Enzymatic activities and DNA substrate specificity of Mycobacterium tuberculosis DNA helicase XPB.

    Directory of Open Access Journals (Sweden)

    Seetha V Balasingham

    Full Text Available XPB, also known as ERCC3 and RAD25, is a 3' → 5' DNA repair helicase belonging to the superfamily 2 of helicases. XPB is an essential core subunit of the eukaryotic basal transcription factor complex TFIIH. It has two well-established functions: in the context of damaged DNA, XPB facilitates nucleotide excision repair by unwinding double stranded DNA (dsDNA surrounding a DNA lesion; while in the context of actively transcribing genes, XPB facilitates initiation of RNA polymerase II transcription at gene promoters. Human and other eukaryotic XPB homologs are relatively well characterized compared to conserved homologs found in mycobacteria and archaea. However, more insight into the function of bacterial helicases is central to understanding the mechanism of DNA metabolism and pathogenesis in general. Here, we characterized Mycobacterium tuberculosis XPB (Mtb XPB, a 3'→5' DNA helicase with DNA-dependent ATPase activity. Mtb XPB efficiently catalyzed DNA unwinding in the presence of significant excess of enzyme. The unwinding activity was fueled by ATP or dATP in the presence of Mg(2+/Mn(2+. Consistent with the 3'→5' polarity of this bacterial XPB helicase, the enzyme required a DNA substrate with a 3' overhang of 15 nucleotides or more. Although Mtb XPB efficiently unwound DNA model substrates with a 3' DNA tail, it was not active on substrates containing a 3' RNA tail. We also found that Mtb XPB efficiently catalyzed ATP-independent annealing of complementary DNA strands. These observations significantly enhance our understanding of the biological roles of Mtb XPB.

  14. Interplay of cis- and trans-regulatory mechanisms in the spliceosomal RNA helicase Brr2.

    Science.gov (United States)

    Absmeier, Eva; Becke, Christian; Wollenhaupt, Jan; Santos, Karine F; Wahl, Markus C

    2017-01-02

    RNA helicase Brr2 is implicated in multiple phases of pre-mRNA splicing and thus requires tight regulation. Brr2 can be auto-inhibited via a large N-terminal region folding back onto its helicase core and auto-activated by a catalytically inactive C-terminal helicase cassette. Furthermore, it can be regulated in trans by the Jab1 domain of the Prp8 protein, which can inhibit Brr2 by intermittently inserting a C-terminal tail in the enzyme's RNA-binding tunnel or activate the helicase after removal of this tail. Presently it is unclear, whether these regulatory mechanisms functionally interact and to which extent they are evolutionarily conserved. Here, we report crystal structures of Saccharomyces cerevisiae and Chaetomium thermophilum Brr2-Jab1 complexes, demonstrating that Jab1-based inhibition of Brr2 presumably takes effect in all eukaryotes but is implemented via organism-specific molecular contacts. Moreover, the structures show that Brr2 auto-inhibition can act in concert with Jab1-mediated inhibition, and suggest that the N-terminal region influences how the Jab1 C-terminal tail interacts at the RNA-binding tunnel. Systematic RNA binding and unwinding studies revealed that the N-terminal region and the Jab1 C-terminal tail specifically interfere with accommodation of double-stranded and single-stranded regions of an RNA substrate, respectively, mutually reinforcing each other. Additionally, such analyses show that regulation based on the N-terminal region requires the presence of the inactive C-terminal helicase cassette. Together, our results outline an intricate system of regulatory mechanisms, which control Brr2 activities during snRNP assembly and splicing.

  15. Effects of Alfalfa Meal on Growth Performance and Gastrointestinal Tract Development of Growing Ducks

    Directory of Open Access Journals (Sweden)

    J. F. Jiang

    2012-10-01

    Full Text Available A study was conducted to evaluate effects of alfalfa meal on growth performance and gastrointestinal tract development of growing layer ducks to provide evidence for application of alfalfa meal in the duck industry. Two hundred and fifty-six healthy Shaoxing 7-wk old growing layer ducks were selected and randomly allocated to 1 of 4 dietary treatments based on corn and soybean meal and containing 0, 3, 6, and 9% of alfalfa meal for 8 wks. Each treatment consisted of 4 replicates of 16 ducks each. Briefly, birds were raised in separate compartments, and each compartment consisted of three parts: indoor floor house, adjacent open area and a connecting water area. The results showed: i Growing ducks fed alfalfa meal diet were not significantly different in average daily gain, feed intake and gain-to-feed ratio from those fed no alfalfa diet (p>0.05. ii Alfalfa meal increased the ratio crop, gizzard to live weight, caecum to live weight, the caecum index of growing ducks (p<0.05. iii Villus height in duodenum and jejunum of growing ducks increased significantly with the increase of alfalfa meal levels (p<0.05. Crypt depth in duodenum and jejunum of growing ducks decreased significantly with the increase of alfalfa meal levels (p<0.05. This experiment showed that feeding of alfalfa meal to growing layer ducks could improve gastrointestinal tract growth and small intestinal morphology without effect on performance. This experiment provides evidence that alfalfa meal is a very valuable feedstuff for growing layer ducks.

  16. Transcriptome of Aphanomyces euteiches: new oomycete putative pathogenicity factors and metabolic pathways.

    Directory of Open Access Journals (Sweden)

    Elodie Gaulin

    Full Text Available Aphanomyces euteiches is an oomycete pathogen that causes seedling blight and root rot of legumes, such as alfalfa and pea. The genus Aphanomyces is phylogenically distinct from well-studied oomycetes such as Phytophthora sp., and contains species pathogenic on plants and aquatic animals. To provide the first foray into gene diversity of A. euteiches, two cDNA libraries were constructed using mRNA extracted from mycelium grown in an artificial liquid medium or in contact to plant roots. A unigene set of 7,977 sequences was obtained from 18,864 high-quality expressed sequenced tags (ESTs and characterized for potential functions. Comparisons with oomycete proteomes revealed major differences between the gene content of A. euteiches and those of Phytophthora species, leading to the identification of biosynthetic pathways absent in Phytophthora, of new putative pathogenicity genes and of expansion of gene families encoding extracellular proteins, notably different classes of proteases. Among the genes specific of A. euteiches are members of a new family of extracellular proteins putatively involved in adhesion, containing up to four protein domains similar to fungal cellulose binding domains. Comparison of A. euteiches sequences with proteomes of fully sequenced eukaryotic pathogens, including fungi, apicomplexa and trypanosomatids, allowed the identification of A. euteiches genes with close orthologs in these microorganisms but absent in other oomycetes sequenced so far, notably transporters and non-ribosomal peptide synthetases, and suggests the presence of a defense mechanism against oxidative stress which was initially characterized in the pathogenic trypanosomatids.

  17. [Population dynamics of ground carabid beetles and spiders in a wheat field along the wheat-alfalfa interface and their response to alfalfa mowing].

    Science.gov (United States)

    Liu, Wen-Hui; Hu, Yi-Jun; Hu, Wen-Chao; Hong, Bo; Guan, Xiao-Qing; Ma, Shi-Yu; He, Da-Han

    2014-09-01

    Taking the wheat-alfalfa and wheat-wheat interfaces as model systems, sampling points were set by the method of pitfall trapping in the wheat field at the distances of 3 m, 6 m, 9 m, 12 m, 15 m, 18 m, 21 m, 24 m, and 27 m from the interface. The species composition and abundance of ground carabid beetles and spiders captured in pitfalls were investigated. The results showed that, to some extent there was an edge effect on species diversity and abundance of ground carabid beetles and spiders along the two interfaces. A marked edge effect was observed between 15 m and 18 m along the alfalfa-wheat interface, while no edge effect was found at a distance over 20 m. The edge effect along the wheat-wheat interface was weaker in comparison to the alfalfa-wheat interface. Alfalfa mowing resulted in the migration of a large number of ground carabid beetles and spiders to the adjacent wheat filed. During ten days since mowing, both species and abundance of ground carabid beetles and spiders increased in wheat filed within the distance of 20 m along the alfalfa-wheat interface. The spatial distribution of species diversity of ground beetles and spiders, together with the population abundance of the dominant Chlaenius pallipes and Pardosa astrigera, were depicted, which could directly indicate the migrating process of natural enemy from alfalfa to wheat field.

  18. Distribution of hydrogen-metabolizing bacteria in alfalfa field soil

    International Nuclear Information System (INIS)

    Cunningham, S.D.; Kapulnik, Y.; Phillips, D.A.

    1986-01-01

    H 2 evolved by alfalfa root nodules during the process of N 2 fixation may be an important factor influencing the distribution of soil bacteria. To test this hypothesis under field conditions, over 700 bacterial isolates were obtained from fallow soil or from the 3-mm layer of soil surrounding alfalfa (Medicago sativa L.) root nodules, alfalfa roots, or bindweed (Convolvulus arvensis L.) roots. Bacteria were isolated under either aerobic or microaerophilic conditions and were tested for their capacity to metabolize H 2 . Isolates showing net H 2 uptake and 3 H 2 incorporation activity under laboratory conditions were assigned a Hup + phenotype, whereas organisms with significant H 2 output capacity were designated as a Hout + phenotype. Under aerobic isolation conditions two Hup + isolates were obtained, whereas under microaerophilic conditions five Hup + and two Hout + isolates were found. The nine isolates differed on the basis of 24 standard bacteriological characteristics or fatty acid composition. Five of the nine organisms were isolated from soil around root nodules, whereas the other four were found distributed among the other three soil environments. On the basis of the microaerophilic isolations, 4.8% of the total procaryotic isolates from soil around root nodules were capable of oxidizing H 2 , and 1.2% could produce H 2 . Two of the Hup + isolates were identified as Rhizobium meliloti by root nodulation tests, but the fact that none of the isolates reduced C 2 H 2 under the assay conditions suggested that the H 2 metabolism traits were associated with various hydrogenase systems rather than with nitrogenase activity

  19. Evaluation of two supplements for the prevention of alfalfa bloat.

    OpenAIRE

    Hall, J W; Walker, I; Majak, W

    1994-01-01

    Poloxalene and a mineral mixture feed supplement patented for the treatment of emphysema, polyarthritis, and other pectin related diseases were tested in two trials for their ability to prevent bloat in cattle fed fresh alfalfa. Each trial had a crossover design using three Jersey steers with rumen fistulas per group. Each trial period continued until the total number of cases of bloat reached > or = 24. Treatments were given at 0800 each day. The mineral mixture was given at 100 g/d and 190 ...

  20. PERACETIC ACID PRETREATMENT OF ALFALFA STEM AND ASPEN BIOMASS

    OpenAIRE

    Lei Xu,; Ulrike W. Tschirner

    2011-01-01

    Alfalfa stems and ground aspen were exposed to peracetic acid (0.5 to 9% on biomass) at temperatures ranging from 40 to 100° C and reaction times from 1 to 5 hours. Glucose release as a percentage of total cellulose content was determined using subsequent standard enzymatic hydrolysis. Statistical analysis confirmed that aspen showed a strong response to peracetic acid addition rate. 9% peracetic acid removed 14% of the original lignin and increased the rate of glucose release from 23% to 44%...

  1. Production of aerial biomass and equivalent land use in alfalfa (Medicago sativa L.) intercropping

    International Nuclear Information System (INIS)

    Pereyra, T. W.; Pagliaricci, H. R.; Ohanian, A. E.; Bonvillani, M. J.

    2013-01-01

    Productivity increase has traditionally been associated to yield increase through breeding and crop management practices. Nevertheless, if production is considered per area and time unit, the intercropping system may be another way to improve cost-effectiveness. The objective of the experiment was to determine the produced biomass and the equivalent land use in alfalfa (Medicago sativa L.) monocrop and intercrops with sorghum Sudan (Sorghum sudanense L.) and oat (Avena sativa L.). The aerial biomass of all the treatments (expressed per surface unit) and the equivalent land use were determined. The design was completely randomized, arranged in blocks with two repetitions. The results were subject to an ANAVA and the means were compared through Duncan's test, by means of the statistical pack INFOSTAT. The alfalfa-sorghum intercrop triplicated the alfalfa production with regards to the monocrop, while alfalfa-oat did not exceed the production of pure alfalfa in the winter months. The alfalfa-sorghum intercrop was 57 % more efficient in land use than the respective monocrops, while alfalfa-oat did not surpass the unit. (author)

  2. Effect of planting patterns on dinitrogen fixation of alfalfa and transfer of N fixed

    International Nuclear Information System (INIS)

    Yao Yunyin; Chen Ming; Zhang Xizhong

    1993-01-01

    Contribution of symbiotic nitrogen fixation of alfalfa grown with different planting patterns was studied in a field experiment. %Ndfa and Ndfa in alfalfa and N transferred from alfalfa in meadow fescue were examined by 2 kinds of 15 N tracer techniques. The superiority of mixed culture of legumes with grasses to monoculture was influenced by planting patterns. Biomass in a mixed culture was related to proportion of alfalfa in it. The proportion of alfalfa was in close relationship not only with ratio of their seeds, but also with planting patterns. Row seeding in mixed seeds was better than broadcasting or intercropping in hay yield, total N yield and %Ndfa and Ndfa. It was also higher than the average of corresponding item of alfalfa and meadow fescue in monoculture each equal area. There was no significantly difference (P 15 N isotope dilution method and natural 1 '5N abundance method. N in meadow fescue transferred from alfalfa could be accurately determined by 15 N isotope diffusion method, but 15 N abundance method gave underestimates, even could not examined N in grasses transferred from associated legumes

  3. Effect of genotype and applied management on alfalfa yield and quality

    Directory of Open Access Journals (Sweden)

    Milić Dragan

    2014-01-01

    Full Text Available It is essential to apply advanced management for successful production of alfalfa hay with premium quality (high content of protein and minerals. The maximum yield and the best quality of alfalfa in Serbia can be obtained by cutting four or five times per year. In alfalfa stands, use of cutting system with three cuts per year is inefficient and does not allow full exploitation of cultivar genetic potential and environmental conditions. It is possible, and economically beneficial to grow alfalfa on pseudoglay soils after application of lime and organic manure, with recommended rates 2.5 t ha-1 lime and 30 t ha-1 manure. Cutting alfalfa at the beginning of flowering stage (5 cuts per year provides hay with better quality - higher content of crude protein and lower portion of fibre fractions (neutral detergent fibre, acid detergent fibre, acid detergent lignin, and there is no reduction in dry matter yield. There is no differences in alfalfa quality after application of lower (2.5 t ha-1 and higher dose (5.0 t ha-1 of lime + 30 t ha-1 of organic manure, but there is significant increase of dry matter yield and protein yield per hectare followed by higher level of metabolic energy per unit area. Upon the results of this study, base of successful alfalfa production would be to develop management system and cultivars for different environments that would maximize hay yields without significant loses of quality.

  4. N resource of grasses and N2-fixation of alfalfa in mono-culture and mixture

    International Nuclear Information System (INIS)

    Zhu Shuxiu

    1992-01-01

    The N behavior in alfalfa and gramineous forage grasses, tall fescue, siberian wild rye, wheat grass and awnless brome were studied in potting and pasture experiments in 1986-1988 by using 15 N isotope dilution technique. Comparison was made between the mixed culture and mono-culture. The % Ndff and %Ndfs of grasses were decreased by 14.19% and 20.76% respectively, while %Ndfa of alfalfa was increased by 20.22% in mixed culture as compared with mono-culture. The 15 N and soil N uptake data revealed that this enhancement was largely due to a lower competitive ability for soil N by alfalfa than by grass in mixed stands, causing the alfalfa to depend more on atmospheric N 2 fixation. 20.62%of N of grasses in mixed culture was from the N 2 -fixation by alfalfa, causing N level in root-sphere of alfalfa decreasing, which was considered to be one of the reasons that %Ndfa increased in mixed culture. N transfer may be carried out by the decomposition of roots and nodules of alfalfa plants

  5. The Undergraduate ALFALFA Team: Outcomes for Over 250 Undergraduate Participants

    Science.gov (United States)

    Troischt, Parker; Koopmann, Rebecca A.; Haynes, Martha P.; ALFALFA Team

    2016-01-01

    The NSF-sponsored Undergraduate ALFALFA (Arecibo Legacy Fast ALFA) Team (UAT) is a consortium of 19 institutions founded to promote undergraduate research and faculty development within the extragalactic ALFALFA HI blind survey project and follow-up programs. In this talk we present outcomes for the more than 250 undergraduate students who have who have participated in the program during the 8 years of funding. 40% of these students have been women and members of underrepresented groups. To date 148 undergraduate students have attended annual workshops at Arecibo Observatory, interacting with faculty, graduate students, their peers, and Arecibo staff in lectures, group activities, tours, and observing runs. Team faculty have supervised 159 summer research projects and 120 academic year (e.g., senior thesis) projects. 68 students have traveled to Arecibo Observatory for observing runs and 55 have presented their results at national meetings such as the AAS. Through participation in the UAT, students are made aware of career paths they may not have previously considered. More than 90% of alumni are attending graduate school and/or pursuing a career in STEM. 42% of those pursuing graduate degrees in Physics or Astronomy are women. This work has been supported by NSF grants AST-0724918/0902211, AST-075267/0903394, AST-0725380, and AST-1211005

  6. Biofertilizer in the nutritional quality of alfalfa (Medicago sativa L.

    Directory of Open Access Journals (Sweden)

    Rodrigo Luis Lemes

    2016-06-01

    Full Text Available The objective of this study was to evaluate the response of alfalfa (Medicago sativa L. in the nutritional composition to the application of biofertilizers. The experiment was conducted with increasing doses of biofertilizers in a greenhouse at the Faculty of Veterinary Medicine / UNESP, Araçatuba - Sao Paulo, Brazil, from April to October 2010. The experimental design was completely randomized with six biofertilizer doses from cattle manure (0, 25, 50, 100, 200, and 400 m3 ha-1 and five replications. Cuts were performed, on average, every 27 days, 10 cm above the ground when 10% of the plants were flowering. Biofertilization had a positive significant impact on foliar nitrogen, potassium, calcium, magnesium, sulfur, and shoot iron concentrations. The values of crude protein, acid detergent fiber, and neutral detergent fiber did not differ between doses of biofertilizers. Biofertilization is a viable alternative for nutrition of this species, showing positive results in the nutritional composition of alfalfa. However, but long-term studies are necessary to assess the environmental impact of these fertilizers.

  7. Evaluation of seed vigor tests for determinig alfalfa seed quality

    Directory of Open Access Journals (Sweden)

    hamidreza tavakoli kakhki

    2009-06-01

    Full Text Available In order to determine the best seed vigor test in laboratory which may provide high correlation between alfalfa seedling stablishment in the field, two experiment were conducted in field as well as in laboratory. Four alfalfa cultivars Bami, Ghareyonjeh, Hamadani and Yazdi were used. Different seed vigor tests including standard germination, germination in low tempretaure (5c , germination rate, osmotic stress, accelerated ageing and electrical conductivity tests were laid out in a randomized completely design (RCD with four replications in laboratory experiment‌. The second experiment was carried out in a randomized completely block design (RCBD and each treatment replicated four times‌. Results revealed significant differences (p≤ 0.01 among different cultivars for establishment percentage and rate. Results also showed that there were significant correlations between electrical conductivity test and establishment percentage (r= -0.65 , p ≤ 0.01 as well as establishment rate (r= -0.80 , p ≤ 0.01. Correlation coefficients for rate and emergence percentage were significant and positive (r= 0.91, p ≤ 0.01 . Stepwise method disclosed that the regression model (y=165.23 – 0.15 x r2=0.64 , (p ≤ 0.01 for predicting rate of emergence could be recommended. In this model x (dependent variable is value of electrical conductivity and y (independent variable is rate of emergence.

  8. DNA secondary structure of the released strand stimulates WRN helicase action on forked duplexes without coordinate action of WRN exonuclease

    Energy Technology Data Exchange (ETDEWEB)

    Ahn, Byungchan, E-mail: bbccahn@mail.ulsan.ac.kr [Department of Life Sciences, University of Ulsan, Ulsan (Korea, Republic of); Bohr, Vilhelm A. [Laboratory of Molecular Gerontology, Biomedical Research Center, National Institute on Aging, Baltimore, MD (United States)

    2011-08-12

    Highlights: {yields} In this study, we investigated the effect of a DNA secondary structure on the two WRN activities. {yields} We found that a DNA secondary structure of the displaced strand during unwinding stimulates WRN helicase without coordinate action of WRN exonuclease. {yields} These results imply that WRN helicase and exonuclease activities can act independently. -- Abstract: Werner syndrome (WS) is an autosomal recessive premature aging disorder characterized by aging-related phenotypes and genomic instability. WS is caused by mutations in a gene encoding a nuclear protein, Werner syndrome protein (WRN), a member of the RecQ helicase family, that interestingly possesses both helicase and exonuclease activities. Previous studies have shown that the two activities act in concert on a single substrate. We investigated the effect of a DNA secondary structure on the two WRN activities and found that a DNA secondary structure of the displaced strand during unwinding stimulates WRN helicase without coordinate action of WRN exonuclease. These results imply that WRN helicase and exonuclease activities can act independently, and we propose that the uncoordinated action may be relevant to the in vivo activity of WRN.

  9. Chemical research of lipophilic fractions of sickle alfalfa herbs

    Directory of Open Access Journals (Sweden)

    S. V. Kovalev

    2013-06-01

    Full Text Available Lipophilic fraction (LF of known medicinal plants are still less studied, despite the fact that they have a unique group of biological active compounds (BAC. The main active substances of LF are chlorophylls, carotenoids, tocopherols, sterols, unsaturated fatty acids, phospholipids, and other bioactive substances that exhibit a wide spectrum of pharmacological action. In this regard, a comprehensive study of advanced plant of flora of Ukraine to increase the assortments of herbal remedies is an urgent problem. The aim of this work was to obtain and chemical research of lipophilic fractions of sickle alfalfa herbs. The alfalfa herb harvested throughout the growing season in Kharkov and Poltava regions in 2011-2012. Lipophilic fraction was obtained by extraction with chloroform in a Soxhlet apparatus. Detection of carotenoids and chlorophylls by thin layer chromatography (TLC on plates of "Silufol" in one-dimensional and two-dimensional variants, the solvent system were: hexane: acetone (6:2 - I way, hexane-acetone (6:4 - II way. Assay of the lipophilic fraction by three-dimensional fluorescence spectroscopy (3DF-spectroscopy was used for the analysis of mixtures containing fluorescent components. 3DF-spectres, that have the appearance of the surface, are characterized by a functions I = f (λexc, λem, recorded in the ultraviolet and visible ranges. Assay of the carotenoids and chlorophylls carried out by spectrophotometry. The reference solution was chloroform. Assay of fatty acids was performed by gas-liquid chromatography (GLC of methyl esters of fatty acids via chromatograph with flame ionization detector "Shimadzu GC-14B". 20.0 g crushed sickle alfalfa herbs were exhaustively extracted with chloroform in a Soxhlet apparatus for produce a lipophilic fractions. The chloroform extract was evaporated in order to remove the extractant. The percentage of lipophilic fraction in the herbs was 7.5%. Quantity of the carotenoids and chlorophylls

  10. Study in mutation of alfalfa genome DNA due to low energy N+ implantation using RAPD

    International Nuclear Information System (INIS)

    Chen Roulei; Song Daojun; Yu Zengliang; Li Yufeng; Liang Yunzhang

    2001-01-01

    After implanted by various dosage N + beams, germination rate of alfalfa seeds appears to be saddle line with dosage increasing. The authors have studied in mutation of genome DNA due to low energy N + implantation, and concluded that 30 differential DNA fragments have been amplified by 8 primers (S 41 , S 42 , S 45 , S 46 , S 50 , S 52 , S 56 , S 58 ) in 100 primers, moreover, number of differential DNA fragments between CK and treatments increases with dosage. Consequently, low energy ion implantation can cause mutation of alfalfa genome DNA. The more dosage it is, the more mutation alfalfa will be

  11. Mycobacterium smegmatis SftH exemplifies a distinctive clade of superfamily II DNA-dependent ATPases with 3′ to 5′ translocase and helicase activities

    OpenAIRE

    Yakovleva, Lyudmila; Shuman, Stewart

    2012-01-01

    Bacterial DNA helicases are nucleic acid-dependent NTPases that play important roles in DNA replication, recombination and repair. We are interested in the DNA helicases of Mycobacteria, a genus of the phylum Actinobacteria, which includes the human pathogen Mycobacterium tuberculosis and its avirulent relative Mycobacterium smegmatis. Here, we identify and characterize M. smegmatis SftH, a superfamily II helicase with a distinctive domain structure, comprising an N-terminal NTPase domain and...

  12. hSSB1 associates with and promotes stability of the BLM helicase

    OpenAIRE

    O'BYRNE, KEN

    2017-01-01

    Background Maintenance of genome stability is critical in human cells. Mutations in or loss of genome stability pathways can lead to a number of pathologies including cancer. hSSB1 is a critical DNA repair protein functioning in the repair and signalling of stalled DNA replication forks, double strand DNA breaks and oxidised DNA lesions. The BLM helicase is central to the repair of both collapsed DNA replication forks and double strand DNA breaks by homologous recombination. Results In this s...

  13. The human RecQ helicases BLM and RECQL4 cooperate to preserve genome stability

    Czech Academy of Sciences Publication Activity Database

    Singh, D.K.; Popuri, V.; Kulikowicz, T.; Shevelev, Igor; Ghosh, A.K.; Ramamoorthy, M.; Rossi, M.L.; Janščák, Pavel; Croteau, D.L.; Bohr, V.A.

    2012-01-01

    Roč. 40, č. 14 (2012), s. 6632-6648 ISSN 0305-1048 R&D Projects: GA ČR GAP305/10/0281 Grant - others:NIH(US) Z01-AG000726-17 Institutional research plan: CEZ:AV0Z50520514 Institutional support: RVO:68378050 Keywords : RecQ helicase * genome stability * BLM * RECQL4 Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 8.278, year: 2012

  14. The eIF4AIII RNA helicase is a critical determinant of human cytomegalovirus replication

    International Nuclear Information System (INIS)

    Ziehr, Ben; Lenarcic, Erik; Cecil, Chad; Moorman, Nathaniel J.

    2016-01-01

    Human cytomegalovirus (HCMV) was recently shown to encode a large number of spliced mRNAs. While the nuclear export of unspliced viral transcripts has been extensively studied, the role of host mRNA export factors in HCMV mRNA trafficking remains poorly defined. We found that the eIF4AIII RNA helicase, a component of the exon junction complex, was necessary for efficient virus replication. Depletion of eIF4AIII limited viral DNA accumulation, export of viral mRNAs from the nucleus, and the production of progeny virus. However eIF4AIII was dispensable for the association of viral transcripts with ribosomes. We found that pateamine A, a natural compound that inhibits both eIF4AI/II and eIF4AIII, has potent antiviral activity and inhibits HCMV replication throughout the virus lytic cycle. Our results demonstrate that eIF4AIII is required for efficient HCMV replication, and suggest that eIF4A family helicases may be a new class of targets for the development of host-directed antiviral therapeutics. - Highlights: • The host eIF4AIII RNA helicase is required for efficient HCMV replication. • Depleting eIF4AIII inhibited the nuclear export of HCMV mRNAs. • HCMV mRNAs did not require eIF4AIII to associate with polyribosomes. • The eIF4A family helicases may be new targets for host-directed antiviral drugs.

  15. Evolution of the DEAD box helicase family in chicken: chickens have no DHX9 ortholog.

    Science.gov (United States)

    Sato, Haruko; Oshiumi, Hiroyuki; Takaki, Hiromi; Hikono, Hirokazu; Seya, Tsukasa

    2015-10-01

    Viral RNA represents a pattern molecule that can be recognized by RNA sensors in innate immunity. Humans and mice possess cytoplasmic DNA/RNA sensors for detecting viral replication. There are a number of DEAD (Asp-Glu-Ala-Asp; DExD/H) box-type helicases in mammals, among which retinoic acid-inducible gene 1 (RIG-I) and melanoma differentiation-associated protein 5 (MDA50) are indispensable for RNA sensing; however, they are functionally supported by a number of sensors that directly bind viral RNA or replicative RNA intermediates to convey signals to RIG-I and MDA5. Some DEAD box helicase members recognize DNA irrespective of the origin. These sensors transmit IFN-inducing signals through adaptors, including mitochondrial antiviral signaling. Viral double-stranded RNAs are reportedly sensed by the helicases DDX1, DDX21, DHX36, DHX9, DDX3, DDX41, LGP2 and DDX60, in addition to RIG-I and MDA5, and induce type I IFNs, thereby blocking viral replication. Humans and mice have all nucleic acid sensors listed here. In the RNA sensing system in chicken, it was found in the present study that most DEAD box helicases are conserved; however, DHX9 is genetically deficient in addition to reported RIG-I. Based on the current genome databases, similar DHX9 deficiency was observed in ducks and several other bird species. Because chicken, but not duck, was found to be deficient in RIG-I, the RNA-sensing system of chicken lacks RIG-I and DHX9 and is thus more fragile than that of duck or mammal. DHX9 may generally compensate for the function of RIG-I and deficiency of DHX9 possibly participates in exacerbations of viral infection such as influenza in chickens. © 2015 The Societies and Wiley Publishing Asia Pty Ltd.

  16. Physical interaction of RECQ5 helicase with RAD51 facilitates its anti-recombinase activity

    Czech Academy of Sciences Publication Activity Database

    Schwendener, S.; Raynard, S.; Paliwal, S.; Cheng, A.; Kanagaraj, R.; Shevelev, Igor; Stark, J.M.; Sung, P.; Janscak, P.

    2010-01-01

    Roč. 285, č. 21 (2010), s. 15739-15745 ISSN 0021-9258 Grant - others:NIH(US) R01CA120954; NIH(US) ES015632; SNSF(CH) 3100A0-116008 Institutional research plan: CEZ:AV0Z50520514 Keywords : DNA helicase * double-strand breaks * homologous recombination Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.328, year: 2010

  17. DEAD-box RNA helicase is dispensable for mitochondrial translation in Trypanosoma brucei

    Czech Academy of Sciences Publication Activity Database

    Richterová, Lenka; Vávrová, Zuzana; Lukeš, Julius

    2011-01-01

    Roč. 127, č. 1 (2011), 300-303 ISSN 0014-4894 R&D Projects: GA ČR GA204/09/1667; GA MŠk LC07032; GA MŠk 2B06129 Institutional research plan: CEZ:AV0Z60220518 Keywords : Trypanosoma * Mitochondrial translation * RNA helicase * Cytochrome c oxidase * Mitochondrion Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.122, year: 2011

  18. The eIF4AIII RNA helicase is a critical determinant of human cytomegalovirus replication

    Energy Technology Data Exchange (ETDEWEB)

    Ziehr, Ben; Lenarcic, Erik; Cecil, Chad; Moorman, Nathaniel J., E-mail: nmoorman@med.unc.edu

    2016-02-15

    Human cytomegalovirus (HCMV) was recently shown to encode a large number of spliced mRNAs. While the nuclear export of unspliced viral transcripts has been extensively studied, the role of host mRNA export factors in HCMV mRNA trafficking remains poorly defined. We found that the eIF4AIII RNA helicase, a component of the exon junction complex, was necessary for efficient virus replication. Depletion of eIF4AIII limited viral DNA accumulation, export of viral mRNAs from the nucleus, and the production of progeny virus. However eIF4AIII was dispensable for the association of viral transcripts with ribosomes. We found that pateamine A, a natural compound that inhibits both eIF4AI/II and eIF4AIII, has potent antiviral activity and inhibits HCMV replication throughout the virus lytic cycle. Our results demonstrate that eIF4AIII is required for efficient HCMV replication, and suggest that eIF4A family helicases may be a new class of targets for the development of host-directed antiviral therapeutics. - Highlights: • The host eIF4AIII RNA helicase is required for efficient HCMV replication. • Depleting eIF4AIII inhibited the nuclear export of HCMV mRNAs. • HCMV mRNAs did not require eIF4AIII to associate with polyribosomes. • The eIF4A family helicases may be new targets for host-directed antiviral drugs.

  19. Distinct functions of human RecQ helicases during DNA replication

    Czech Academy of Sciences Publication Activity Database

    Urban, Václav; Dobrovolná, Jana; Janščák, Pavel

    2017-01-01

    Roč. 225, červen (2017), s. 20-26 ISSN 0301-4622 R&D Projects: GA ČR(CZ) GA14-05743S; GA MŠk LH14037 Institutional support: RVO:68378050 Keywords : DNA replication * Replication stress * RecQ helicases * Genomic instability * Cancer Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemistry and molecular biology Impact factor: 2.402, year: 2016

  20. Relocalization of nuclear DNA helicase II during the growth period of bovine oocytes

    Czech Academy of Sciences Publication Activity Database

    Baran, V.; Kovářová, Hana; Klíma, Jiří; Hozák, Pavel; Motlík, Jan

    2006-01-01

    Roč. 125, 1-2 (2006), s. 155-164 ISSN 0948-6143 R&D Projects: GA ČR GA523/03/0857 Grant - others:Slovenská Akademie věd(SK) VEGA 2/3065/23 Institutional research plan: CEZ:AV0Z50450515; CEZ:AV0Z50390512 Keywords : DNA helicase II * fibroblasts * oocytes Subject RIV: EB - Genetics ; Molecular Biology Impact factor : 3.220, year: 2006

  1. Senataxin, the ortholog of a yeast RNA helicase, is mutant in ataxia-ocular apraxia 2.

    Science.gov (United States)

    Moreira, Maria-Céu; Klur, Sandra; Watanabe, Mitsunori; Németh, Andrea H; Le Ber, Isabelle; Moniz, José-Carlos; Tranchant, Christine; Aubourg, Patrick; Tazir, Meriem; Schöls, Lüdger; Pandolfo, Massimo; Schulz, Jörg B; Pouget, Jean; Calvas, Patrick; Shizuka-Ikeda, Masami; Shoji, Mikio; Tanaka, Makoto; Izatt, Louise; Shaw, Christopher E; M'Zahem, Abderrahim; Dunne, Eimear; Bomont, Pascale; Benhassine, Traki; Bouslam, Naïma; Stevanin, Giovanni; Brice, Alexis; Guimarães, João; Mendonça, Pedro; Barbot, Clara; Coutinho, Paula; Sequeiros, Jorge; Dürr, Alexandra; Warter, Jean-Marie; Koenig, Michel

    2004-03-01

    Ataxia-ocular apraxia 2 (AOA2) was recently identified as a new autosomal recessive ataxia. We have now identified causative mutations in 15 families, which allows us to clinically define this entity by onset between 10 and 22 years, cerebellar atrophy, axonal sensorimotor neuropathy, oculomotor apraxia and elevated alpha-fetoprotein (AFP). Ten of the fifteen mutations cause premature termination of a large DEAxQ-box helicase, the human ortholog of yeast Sen1p, involved in RNA maturation and termination.

  2. Role of the hydrophilic channels of simian virus 40 T-antigen helicase in DNA replication.

    Science.gov (United States)

    Wang, Weiping; Manna, David; Simmons, Daniel T

    2007-05-01

    The simian virus 40 (SV40) hexameric helicase consists of a central channel and six hydrophilic channels located between adjacent large tier domains within each hexamer. To study the function of the hydrophilic channels in SV40 DNA replication, a series of single-point substitutions were introduced at sites not directly involved in protein-protein contacts. The mutants were characterized biochemically in various ways. All mutants oligomerized normally in the absence of DNA. Interestingly, 8 of the 10 mutants failed to unwind an origin-containing DNA fragment and nine of them were totally unable to support SV40 DNA replication in vitro. The mutants fell into four classes based on their biochemical properties. Class A mutants bound DNA normally and had normal ATPase and helicase activities but failed to unwind origin DNA and support SV40 DNA replication. Class B mutants were compromised in single-stranded DNA and origin DNA binding at low protein concentrations. They were defective in helicase activity and unwinding of the origin and in supporting DNA replication. Class C and D mutants possessed higher-than-normal single-stranded DNA binding activity at low protein concentrations. The class C mutants failed to separate origin DNA and support DNA replication. The class D mutants unwound origin DNA normally but were compromised in their ability to support DNA replication. Taken together, these results suggest that the hydrophilic channels have an active role in the unwinding of SV40 DNA from the origin and the placement of the resulting single strands within the helicase.

  3. RTEL1: an essential helicase for telomere maintenance and the regulation of homologous recombination

    OpenAIRE

    Uringa, Evert-Jan; Youds, Jillian L.; Lisaingo, Kathleen; Lansdorp, Peter M.; Boulton, Simon J.

    2010-01-01

    Telomere maintenance and DNA repair are crucial processes that protect the genome against instability. RTEL1, an essential iron–sulfur cluster-containing helicase, is a dominant factor that controls telomere length in mice and is required for telomere integrity. In addition, RTEL1 promotes synthesis-dependent strand annealing to direct DNA double-strand breaks into non-crossover outcomes during mitotic repair and in meiosis. Here, we review the role of RTEL1 in telomere maintenance and homolo...

  4. Alfalfa (Medicago sativa L.) shoot saponins: identification and bio-activity by the assessment of aphid feeding.

    Science.gov (United States)

    Mazahery-Laghab, H; Yazdi-Samadi, B; Bagheri, M; Bagheri, A R

    2011-01-01

    Biochemical components in alfalfa (Medicago sativa L.), such as saponins, can act as protecting factors against bio-stresses. Saponins are also antifeedants and show oral toxicity towards higher and lower animals. Changes in saponins, such as variation in the carbon skeleton, or hydrolysis of saponin glycosides and other conjugates, may change their biological effects. The aims of this research were to study saponin variation in different growth stages of alfalfa and to investigate the biological role of saponins in the spotted alfalfa aphid, Therioaphis maculata. Saponins from alfalfa shoots in different growth stages were extracted, chemically purified and analysed by TLC. Specific saponins such as soyasaponin1 from root and shoot and two bisdesmosides of medicagenic acid, one from shoot and another from root tissues, were identified using reference compounds allowing changes in saponin composition during plant development in different shoot tissues of alfalfa to be assessed. The response of the alfalfa aphid to feeding on alfalfa in different growth stages was studied. No significant difference in the survival of aphids, from neonate to adult, was observed, but due to the antibiotic effects of saponins, two differences were found in the onset of nymph production and cumulative nymph production. The results show that the saponin composition in alfalfa changes with plant development and this, in turn, can often negatively affect the development of specific insect pests such as the spotted alfalfa aphid, suggesting a possible biological role of alfalfa saponins.

  5. Archaeal MCM Proteins as an Analog for the Eukaryotic Mcm2–7 Helicase to Reveal Essential Features of Structure and Function

    Science.gov (United States)

    Miller, Justin M.; Enemark, Eric J.

    2015-01-01

    In eukaryotes, the replicative helicase is the large multisubunit CMG complex consisting of the Mcm2–7 hexameric ring, Cdc45, and the tetrameric GINS complex. The Mcm2–7 ring assembles from six different, related proteins and forms the core of this complex. In archaea, a homologous MCM hexameric ring functions as the replicative helicase at the replication fork. Archaeal MCM proteins form thermostable homohexamers, facilitating their use as models of the eukaryotic Mcm2–7 helicase. Here we review archaeal MCM helicase structure and function and how the archaeal findings relate to the eukaryotic Mcm2–7 ring. PMID:26539061

  6. Complete nucleotide sequence and genome organization of Olive latent virus 3, a new putative member of the family Tymoviridae.

    Science.gov (United States)

    Alabdullah, Abdulkader; Minafra, Angelantonio; Elbeaino, Toufic; Saponari, Maria; Savino, Vito; Martelli, Giovanni P

    2010-09-01

    The complete nucleotide sequence and the genome organization were determined of a putative new member of the family Tymoviridae, tentatively named Olive latent virus 3 (OLV-3), recovered in southern Italy from a symptomless olive tree. The sequenced ssRNA genome comprises 7148 nucleotides excluding the poly(A) tail and contains four open reading frames (ORFs). ORF1 encodes a polyprotein of 221.6kDa in size, containing the conserved signatures of the methyltransferase (MTR), papain-like protease (PRO), helicase (HEL) and RNA-dependent RNA polymerase (RdRp) domains of the replication-associated proteins of positive-strand RNA viruses. ORF2 overlaps completely ORF1 and encodes a putative protein of 43.33kDa showing limited sequence similarity with the putative movement protein of Maize rayado fino virus (MRFV). ORF3 codes for a protein with predicted molecular mass of 28.46kDa, identified as the coat protein (CP), whereas ORF4 overlaps ORF3 and encodes a putative protein of 16kDa with sequence similarity to the p16 and p31 proteins of Citrus sudden death-associated virus (CSDaV) and Grapevine fleck virus (GFkV), respectively. Within the family Tymoviridae, OLV-3 genome has the closest identity level (49-52%) with members of the genus Marafivirus, from which, however, it differs because of the diverse genome organization and the presence of a single type of CP subunits. Copyright (c) 2010 Elsevier B.V. All rights reserved.

  7. Escherichia coli and Neisseria gonorrhoeae UvrD helicase unwinds G4 DNA structures.

    Science.gov (United States)

    Shukla, Kaustubh; Thakur, Roshan Singh; Ganguli, Debayan; Rao, Desirazu Narasimha; Nagaraju, Ganesh

    2017-10-18

    G-quadruplex (G4) secondary structures have been implicated in various biological processes, including gene expression, DNA replication and telomere maintenance. However, unresolved G4 structures impede replication progression which can lead to the generation of DNA double-strand breaks and genome instability. Helicases have been shown to resolve G4 structures to facilitate faithful duplication of the genome. Escherichia coli UvrD (EcUvrD) helicase plays a crucial role in nucleotide excision repair, mismatch repair and in the regulation of homologous recombination. Here, we demonstrate a novel role of E. coli and Neisseria gonorrhoeae UvrD in resolving G4 tetraplexes. EcUvrD and N gonorrhoeae UvrD were proficient in unwinding previously characterized tetramolecular G4 structures. Notably, EcUvrD was equally efficient in resolving tetramolecular and bimolecular G4 DNA that were derived from the potential G4-forming sequences from the genome of E. coli Interestingly, in addition to resolving intermolecular G4 structures, EcUvrD was robust in unwinding intramolecular G4 structures. These data for the first time provide evidence for the role of UvrD in the resolution of G4 structures, which has implications for the in vivo role of UvrD helicase in G4 DNA resolution and genome maintenance. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  8. The helicase domain of Polθ counteracts RPA to promote alt-NHEJ.

    Science.gov (United States)

    Mateos-Gomez, Pedro A; Kent, Tatiana; Deng, Sarah K; McDevitt, Shane; Kashkina, Ekaterina; Hoang, Trung M; Pomerantz, Richard T; Sfeir, Agnel

    2017-12-01

    Mammalian polymerase theta (Polθ) is a multifunctional enzyme that promotes error-prone DNA repair by alternative nonhomologous end joining (alt-NHEJ). Here we present structure-function analyses that reveal that, in addition to the polymerase domain, Polθ-helicase activity plays a central role during double-strand break (DSB) repair. Our results show that the helicase domain promotes chromosomal translocations by alt-NHEJ in mouse embryonic stem cells and also suppresses CRISPR-Cas9- mediated gene targeting by homologous recombination (HR). In vitro assays demonstrate that Polθ-helicase activity facilitates the removal of RPA from resected DSBs to allow their annealing and subsequent joining by alt-NHEJ. Consistent with an antagonistic role for RPA during alt-NHEJ, inhibition of RPA1 enhances end joining and suppresses recombination. Taken together, our results reveal that the balance between HR and alt-NHEJ is controlled by opposing activities of Polθ and RPA, providing further insight into the regulation of repair-pathway choice in mammalian cells.

  9. Non-B DNA Secondary Structures and Their Resolution by RecQ Helicases

    Directory of Open Access Journals (Sweden)

    Sudha Sharma

    2011-01-01

    Full Text Available In addition to the canonical B-form structure first described by Watson and Crick, DNA can adopt a number of alternative structures. These non-B-form DNA secondary structures form spontaneously on tracts of repeat sequences that are abundant in genomes. In addition, structured forms of DNA with intrastrand pairing may arise on single-stranded DNA produced transiently during various cellular processes. Such secondary structures have a range of biological functions but also induce genetic instability. Increasing evidence suggests that genomic instabilities induced by non-B DNA secondary structures result in predisposition to diseases. Secondary DNA structures also represent a new class of molecular targets for DNA-interactive compounds that might be useful for targeting telomeres and transcriptional control. The equilibrium between the duplex DNA and formation of multistranded non-B-form structures is partly dependent upon the helicases that unwind (resolve these alternate DNA structures. With special focus on tetraplex, triplex, and cruciform, this paper summarizes the incidence of non-B DNA structures and their association with genomic instability and emphasizes the roles of RecQ-like DNA helicases in genome maintenance by resolution of DNA secondary structures. In future, RecQ helicases are anticipated to be additional molecular targets for cancer chemotherapeutics.

  10. Structural mechanisms of human RecQ helicases WRN and BLM

    Directory of Open Access Journals (Sweden)

    Ken eKitano

    2014-10-01

    Full Text Available The RecQ family DNA helicases WRN (Werner syndrome protein and BLM (Bloom syndrome protein play a key role in protecting the genome against deleterious changes. In humans, mutations in these proteins lead to rare genetic diseases associated with cancer predisposition and accelerated aging. WRN and BLM are distinguished from other helicases by possessing signature tandem domains toward the C terminus, referred to as the RecQ C-terminal (RQC and helicase-and-ribonuclease D-C-terminal (HRDC domains. Although the precise function of the HRDC domain remains unclear, the previous crystal structure of a WRN RQC-DNA complex visualized a central role for the RQC domain in recognizing, binding and unwinding DNA at branch points. In particular, a prominent hairpin structure (the β-wing within the RQC winged-helix motif acts as a scalpel to induce the unpairing of a Watson-Crick base pair at the DNA duplex terminus. A similar RQC-DNA interaction was also observed in the recent crystal structure of a BLM-DNA complex. I review the latest structures of WRN and BLM, and then provide a docking simulation of BLM with a Holliday junction. The model offers an explanation for the efficient branch migration activity of the RecQ family toward recombination and repair intermediates.

  11. Novel benzoxazole inhibitor of dengue virus replication that targets the NS3 helicase.

    Science.gov (United States)

    Byrd, Chelsea M; Grosenbach, Douglas W; Berhanu, Aklile; Dai, Dongcheng; Jones, Kevin F; Cardwell, Kara B; Schneider, Christine; Yang, Guang; Tyavanagimatt, Shanthakumar; Harver, Chris; Wineinger, Kristin A; Page, Jessica; Stavale, Eric; Stone, Melialani A; Fuller, Kathleen P; Lovejoy, Candace; Leeds, Janet M; Hruby, Dennis E; Jordan, Robert

    2013-04-01

    Dengue virus (DENV) is the predominant mosquito-borne viral pathogen that infects humans with an estimated 50 to 100 million infections per year worldwide. Over the past 50 years, the incidence of dengue disease has increased dramatically and the virus is now endemic in more than 100 countries. Moreover, multiple serotypes of DENV are now found in the same geographic region, increasing the likelihood of more severe forms of disease. Despite extensive research, there are still no approved vaccines or therapeutics commercially available to treat DENV infection. Here we report the results of a high-throughput screen of a chemical compound library using a whole-virus assay that identified a novel small-molecule inhibitor of DENV, ST-610, that potently and selectively inhibits all four serotypes of DENV replication in vitro. Sequence analysis of drug-resistant virus isolates has identified a single point mutation, A263T, in the NS3 helicase domain that confers resistance to this compound. ST-610 inhibits DENV NS3 helicase RNA unwinding activity in a molecular-beacon-based helicase assay but does not inhibit nucleoside triphosphatase activity based on a malachite green ATPase assay. ST-610 is nonmutagenic, is well tolerated (nontoxic) in mice, and has shown efficacy in a sublethal murine model of DENV infection with the ability to significantly reduce viremia and viral load compared to vehicle controls.

  12. Helicase properties of the Escherichia coli UvrAb protein complex

    International Nuclear Information System (INIS)

    Oh, E.Y.; Grossman, L.

    1987-01-01

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

  13. Staphylococcal SCCmec elements encode an active MCM-like helicase and thus may be replicative

    Energy Technology Data Exchange (ETDEWEB)

    Mir-Sanchis, Ignacio; Roman, Christina A.; Misiura, Agnieszka; Pigli, Ying Z.; Boyle-Vavra, Susan; Rice , Phoebe A. (UC)

    2016-08-29

    Methicillin-resistant Staphylococcus aureus (MRSA) is a public-health threat worldwide. Although the mobile genomic island responsible for this phenotype, staphylococcal cassette chromosome (SCC), has been thought to be nonreplicative, we predicted DNA-replication-related functions for some of the conserved proteins encoded by SCC. We show that one of these, Cch, is homologous to the self-loading initiator helicases of an unrelated family of genomic islands, that it is an active 3'-to-5' helicase and that the adjacent ORF encodes a single-stranded DNA–binding protein. Our 2.9-Å crystal structure of intact Cch shows that it forms a hexameric ring. Cch, like the archaeal and eukaryotic MCM-family replicative helicases, belongs to the pre–sensor II insert clade of AAA+ ATPases. Additionally, we found that SCC elements are part of a broader family of mobile elements, all of which encode a replication initiator upstream of their recombinases. Replication after excision would enhance the efficiency of horizontal gene transfer.

  14. A new role for FBP21 as regulator of Brr2 helicase activity.

    Science.gov (United States)

    Henning, Lisa M; Santos, Karine F; Sticht, Jana; Jehle, Stefanie; Lee, Chung-Tien; Wittwer, Malte; Urlaub, Henning; Stelzl, Ulrich; Wahl, Markus C; Freund, Christian

    2017-07-27

    Splicing of eukaryotic pre-mRNA is carried out by the spliceosome, which assembles stepwise on each splicing substrate. This requires the concerted action of snRNPs and non-snRNP accessory proteins, the functions of which are often not well understood. Of special interest are B complex factors that enter the spliceosome prior to catalytic activation and may alter splicing kinetics and splice site selection. One of these proteins is FBP21, for which we identified several spliceosomal binding partners in a yeast-two-hybrid screen, among them the RNA helicase Brr2. Biochemical and biophysical analyses revealed that an intrinsically disordered region of FBP21 binds to an extended surface of the C-terminal Sec63 unit of Brr2. Additional contacts in the C-terminal helicase cassette are required for allosteric inhibition of Brr2 helicase activity. Furthermore, the direct interaction between FBP21 and the U4/U6 di-snRNA was found to reduce the pool of unwound U4/U6 di-snRNA. Our results suggest FBP21 as a novel key player in the regulation of Brr2. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Posttranscriptional regulation of the karyogamy gene by Kem1p/Xrn1p exoribonuclease and Rok1p RNA helicase of Saccharomyces cerevisiae

    International Nuclear Information System (INIS)

    Kim, Jaehee; Jeon, Soonmee; Yang, Yun-Seok; Kim, Jinmi

    2004-01-01

    The major biochemical activities ascribed to Kem1p/Xrn1p of Saccharomyces cerevisiae are 5'-3' exoribonuclease functioning in RNA turnover and a microtubule-binding protein. Mutational analysis has shown that Kem1p/Xrn1p participates in microtubule-related functions such as nuclear fusion (karyogamy) during mating, chromosome transmission, and spindle pole body duplication. Here, evidence is presented that Kem1p plays a specific role in nuclear fusion by affecting, at the posttranscriptional level, the pheromone induction of the karyogamy-specific transcription factor Kar4p and the expression of Rok1p, a putative RNA helicase. We found that Rok1p itself also affects the pheromone induction of Kar4p and thereby participates in nuclear fusion. Analysis of the active-site mutations, xrn1-D206A or D208A, shows that nuclear fusion as well as the Rok1p synthesis do not require the exoribonuclease activity of Kem1p. Our data provide an important insight into the gene-specific regulatory function mediated by the general RNA-modulating enzymes

  16. Deficiency of the Arabidopsis helicase RTEL1 triggers a SOG1-dependent replication checkpoint in response to DNA cross-links.

    Science.gov (United States)

    Hu, Zhubing; Cools, Toon; Kalhorzadeh, Pooneh; Heyman, Jefri; De Veylder, Lieven

    2015-01-01

    To maintain genome integrity, DNA replication is executed and regulated by a complex molecular network of numerous proteins, including helicases and cell cycle checkpoint regulators. Through a systematic screening for putative replication mutants, we identified an Arabidopsis thaliana homolog of human Regulator of Telomere Length 1 (RTEL1), which functions in DNA replication, DNA repair, and recombination. RTEL1 deficiency retards plant growth, a phenotype including a prolonged S-phase duration and decreased cell proliferation. Genetic analysis revealed that rtel1 mutant plants show activated cell cycle checkpoints, specific sensitivity to DNA cross-linking agents, and increased homologous recombination, but a lack of progressive shortening of telomeres, indicating that RTEL1 functions have only been partially conserved between mammals and plants. Surprisingly, RTEL1 deficiency induces tolerance to the deoxynucleotide-depleting drug hydroxyurea, which could be mimicked by DNA cross-linking agents. This resistance does not rely on the essential replication checkpoint regulator WEE1 but could be blocked by a mutation in the SOG1 transcription factor. Taken together, our data indicate that RTEL1 is required for DNA replication and that its deficiency activates a SOG1-dependent replication checkpoint. © 2015 American Society of Plant Biologists. All rights reserved.

  17. PENINGKATAN PRODUKSI DAN KECERNAAN BAHAN KERING ALFALFA DENGAN PEMUPUKAN FOSFAT

    Directory of Open Access Journals (Sweden)

    - Sunarni

    2014-06-01

    Full Text Available Alfalfa (Medicago    sativa    L. as one of legume forage crops for ruminant livestock is very sensitive to the phosphorus deficiency. Phosphorus fertilizers have been used widely to overcome those problem. However, the high cost of superphosphate (SP is now focusing attention on cheaper rock phosphate (RP fertilizer. A field experiment was conducted on a latosolic soil (low pH, and low available Bray II extractable P. The objective of the research is to evaluate the effect of phosphorus fertilizer from difference sources on dry matter production, and in    vitro dry matter digestibility of alfalfa. Completely randomized block design with 7 treatments in 3 replicates was used in this field experiment. The treatments were T0 (control, T1 (SP, 100 kg P2O5/ha, T2 (SP, 200 kg P2O5/ha, T3 (SP, 300 kg P2O5/ha, T4 (RP, 100 kg P2O5/ha, T5 (RP, 200 kg P2O5/ha, T6 (RP, 300 kg P2O5/ha. Size of each plot was 2 m x 2 m, and fertilized with P fertilizer (SP, RP according to the assigned treatment. All plot received basal fertilizer of urea (50 kg N/ha, KCl (100 kg K2O/ha and poultry manure (2 ton/ha. Medicago    sativa was defoliated on 12 weeks after planting and analyzed for dry matter (DM production and in    vitro DM digestibility. Result showed that DM production significantly influenced by the treatments. Superphosphate fertilization resulted DM production significantly higher compared to control and RP, except on RP 300 kg P2O5/ha was non-significant difference. In    vitro dry matter digestibility (IVDMD of alfalfa was not affected by the treatment. There was non-significant difference in IVDMD between the treatments. Therefore, RP (300 kg P2O5/ha could replace SP to increased DM production and not affected for IVDMD of Medicago    sativa in acid latosolic soil.

  18. Mezclas de Alfalfa y Gramíneas en la Serie Sabana de Bogotá Tipo Franco Arcilloso.

    Directory of Open Access Journals (Sweden)

    Chaverra Gil. Hernán

    1960-06-01

    Full Text Available En el Centro Nacional de Investigaciones Agrícolas, Tibaitatá, y en la serie de suelos Sabana de Bogotá, tipo frnaco arcilloso, se llevaron a cabo dos experimentos con mezclas de alfalfa y gramíneas. En el primer ensayo, se sembraron simultáneamente con la alfalfa, ryegrass inglés, rygrass anual y orchoso. Los métodos de siembra utilizados fueron: a alfalfa y gramíneas sembradas al voleo, b alfalfa y gramíneas en el mismo surco, c alfalfa y gramíneas en surcos alternos, d alfalfa en surcos y gramíneas al voleo y e alfalfa en surcos y trébol blanco al voleo. En el segundo experimento se sembró la alfalfa en surcos separados 25 cm. Después de establecida la alfalfa e inmediatamente después del 4° corte se sembraron al voleo las siguientes gramíneas: ryegrass inglés, rygrass anual, orchoro, festuca media, pasto cinta y pasto rescate. Las finalidades del estudio fueron las de valorar el comportamiento de las gramíneas en mezcla con la alfalfa, mediante la determinación progresiva de la composición botánica y el rendimiento de forraje seco de las mezclas. La siembra simultánea de ryegrass inglés y ryegrass anual con la alfalfa dio como resultado una mala población de la leguminosa, especialmente en los dos primeros cortes. La competencia ejercida por estas dos gramíneas a la alfalfa, se redujo casi completamente, cuando se sembraron en surcos alternos o en la alfalfa establecida. Sea cual fuere el pasto sembrado, la siembra de gramíneas en alfalfa establecida, redujo la competencia entre los pastos asociados. En este ensayo el factor más importante en el establecimiento de las gramíneas, fue el agua disponible en el suelo. Bajo las condiciones del primer experimento el orchoro fue la gramínea que mejor creció en asocio de la alfalfa en todos los métodos de siembra estudiado. La producción promedia de la mezcla varió entre 2600 y 3145 Kg/hect. De forreje seco por corte y la proporción de orchoro entre

  19. Easy synthesis of graphene sheets from alfalfa plants by treatment of nitric acid

    International Nuclear Information System (INIS)

    Qu, Jiao; Luo, Chunqiu; Zhang, Qian; Cong, Qiao; Yuan, Xing

    2013-01-01

    Highlights: ► An easy method for synthesis of graphene sheets using alfalfa plants was introduced. ► An novelty formation mechanism of graphene sheets using alfalfa plants was proposed. ► This method exploits a new carbon source and provides a novel idea to synthesize graphene sheets. -- Abstract: This letter focuses on synthesis of graphene sheets from alfalfa plants by treatment of nitric acid. The transmission electron microscopy image (TEM) demonstrates that the graphene sheets are agglomerated and overlapped, the energy dispersive spectrum (EDS) indicates that the products are pure, and the Raman spectrum shows the graphene sheets are well graphitized. In addition, the formation mechanism of the graphene sheets from alfalfa plants by treatment nitric acid is discussed. These findings inspire the search for a new strategy for synthesis of graphene sheets from renewable natural products, and the lower cost of this new process and carbon source may facilitate industrial production

  20. Easy synthesis of graphene sheets from alfalfa plants by treatment of nitric acid

    Energy Technology Data Exchange (ETDEWEB)

    Qu, Jiao, E-mail: qujiao@bhu.edu.cn [School of Chemistry and Chemical Engineering, Bohai University, Jinzhou 121013 (China); School of Urban and Environmental Sciences, Northeast Normal University, Changchun 130024 (China); Luo, Chunqiu, E-mail: fplj_lcq@163.com [School of Chemistry and Chemical Engineering, Bohai University, Jinzhou 121013 (China); Zhang, Qian; Cong, Qiao [School of Chemistry and Chemical Engineering, Bohai University, Jinzhou 121013 (China); Yuan, Xing [School of Urban and Environmental Sciences, Northeast Normal University, Changchun 130024 (China)

    2013-04-01

    Highlights: ► An easy method for synthesis of graphene sheets using alfalfa plants was introduced. ► An novelty formation mechanism of graphene sheets using alfalfa plants was proposed. ► This method exploits a new carbon source and provides a novel idea to synthesize graphene sheets. -- Abstract: This letter focuses on synthesis of graphene sheets from alfalfa plants by treatment of nitric acid. The transmission electron microscopy image (TEM) demonstrates that the graphene sheets are agglomerated and overlapped, the energy dispersive spectrum (EDS) indicates that the products are pure, and the Raman spectrum shows the graphene sheets are well graphitized. In addition, the formation mechanism of the graphene sheets from alfalfa plants by treatment nitric acid is discussed. These findings inspire the search for a new strategy for synthesis of graphene sheets from renewable natural products, and the lower cost of this new process and carbon source may facilitate industrial production.

  1. Impact of Bee Species and Plant Density on Alfalfa Pollination and Potential for Gene Flow

    Directory of Open Access Journals (Sweden)

    Johanne Brunet

    2010-01-01

    Full Text Available In outcrossing crops like alfalfa, various bee species can contribute to pollination and gene flow in seed production fields. With the increasing use of transgenic crops, it becomes important to determine the role of these distinct pollinators on alfalfa pollination and gene flow. The current study examines the relative contribution of honeybees, three bumble bee species, and three solitary bee species to pollination and gene flow in alfalfa. Two wild solitary bee species and one wild bumble bee species were best at tripping flowers, while the two managed pollinators commonly used in alfalfa seed production, honeybees and leaf cutting bees, had the lowest tripping rate. Honeybees had the greatest potential for gene flow and risk of transgene escape relative to the other pollinators. For honeybees, gene flow and risk of transgene escape were not affected by plant density although for the three bumble bee species gene flow and risk of transgene escape were the greatest in high-density fields.

  2. A holistic evolutionary and structural study of flaviviridae provides insights into the function and inhibition of HCV helicase

    Directory of Open Access Journals (Sweden)

    Dimitrios Vlachakis

    2013-05-01

    Full Text Available Viral RNA helicases are involved in duplex unwinding during the RNA replication of the virus. It is suggested that these helicases represent very promising antiviral targets. Viruses of the flaviviridae family are the causative agents of many common and devastating diseases, including hepatitis, yellow fever and dengue fever. As there is currently no available anti-Flaviviridae therapy, there is urgent need for the development of efficient anti-viral pharmaceutical strategies. Herein, we report the complete phylogenetic analysis across flaviviridae alongside a more in-depth evolutionary study that revealed a series of conserved and invariant amino acids that are predicted to be key to the function of the helicase. Structural molecular modelling analysis revealed the strategic significance of these residues based on their relative positioning on the 3D structures of the helicase enzymes, which may be used as pharmacological targets. We previously reported a novel series of highly potent HCV helicase inhibitors, and we now re-assess their antiviral potential using the 3D structural model of the invariant helicase residues. It was found that the most active compound of the series, compound C4, exhibited an IC50 in the submicromolar range, whereas its stereoisomer (compound C12 was completely inactive. Useful insights were obtained from molecular modelling and conformational search studies via molecular dynamics simulations. C12 tends to bend and lock in an almost “U” shape conformation, failing to establish vital interactions with the active site of HCV. On the contrary, C4 spends most of its conformational time in a straight, more rigid formation that allows it to successfully block the passage of the oligonucleotide in the ssRNA channel of the HCV helicase. This study paves the way and provides the necessary framework for the in-depth analysis required to enable the future design of new and potent anti-viral agents.

  3. DNA unwinding by ring-shaped T4 helicase gp41 is hindered by tension on the occluded strand.

    Science.gov (United States)

    Ribeck, Noah; Saleh, Omar A

    2013-01-01

    The replicative helicase for bacteriophage T4 is gp41, which is a ring-shaped hexameric motor protein that achieves unwinding of dsDNA by translocating along one strand of ssDNA while forcing the opposite strand to the outside of the ring. While much study has been dedicated to the mechanism of binding and translocation along the ssDNA strand encircled by ring-shaped helicases, relatively little is known about the nature of the interaction with the opposite, 'occluded' strand. Here, we investigate the interplay between the bacteriophage T4 helicase gp41 and the ss/dsDNA fork by measuring, at the single-molecule level, DNA unwinding events on stretched DNA tethers in multiple geometries. We find that gp41 activity is significantly dependent on the geometry and tension of the occluded strand, suggesting an interaction between gp41 and the occluded strand that stimulates the helicase. However, the geometry dependence of gp41 activity is the opposite of that found previously for the E. coli hexameric helicase DnaB. Namely, tension applied between the occluded strand and dsDNA stem inhibits unwinding activity by gp41, while tension pulling apart the two ssDNA tails does not hinder its activity. This implies a distinct variation in helicase-occluded strand interactions among superfamily IV helicases, and we propose a speculative model for this interaction that is consistent with both the data presented here on gp41 and the data that had been previously reported for DnaB.

  4. Human Enterovirus Nonstructural Protein 2CATPase Functions as Both an RNA Helicase and ATP-Independent RNA Chaperone

    Science.gov (United States)

    Xia, Hongjie; Wang, Peipei; Wang, Guang-Chuan; Yang, Jie; Sun, Xianlin; Wu, Wenzhe; Qiu, Yang; Shu, Ting; Zhao, Xiaolu; Yin, Lei; Qin, Cheng-Feng; Hu, Yuanyang; Zhou, Xi

    2015-01-01

    RNA helicases and chaperones are the two major classes of RNA remodeling proteins, which function to remodel RNA structures and/or RNA-protein interactions, and are required for all aspects of RNA metabolism. Although some virus-encoded RNA helicases/chaperones have been predicted or identified, their RNA remodeling activities in vitro and functions in the viral life cycle remain largely elusive. Enteroviruses are a large group of positive-stranded RNA viruses in the Picornaviridae family, which includes numerous important human pathogens. Herein, we report that the nonstructural protein 2CATPase of enterovirus 71 (EV71), which is the major causative pathogen of hand-foot-and-mouth disease and has been regarded as the most important neurotropic enterovirus after poliovirus eradication, functions not only as an RNA helicase that 3′-to-5′ unwinds RNA helices in an adenosine triphosphate (ATP)-dependent manner, but also as an RNA chaperone that destabilizes helices bidirectionally and facilitates strand annealing and complex RNA structure formation independently of ATP. We also determined that the helicase activity is based on the EV71 2CATPase middle domain, whereas the C-terminus is indispensable for its RNA chaperoning activity. By promoting RNA template recycling, 2CATPase facilitated EV71 RNA synthesis in vitro; when 2CATPase helicase activity was impaired, EV71 RNA replication and virion production were mostly abolished in cells, indicating that 2CATPase-mediated RNA remodeling plays a critical role in the enteroviral life cycle. Furthermore, the RNA helicase and chaperoning activities of 2CATPase are also conserved in coxsackie A virus 16 (CAV16), another important enterovirus. Altogether, our findings are the first to demonstrate the RNA helicase and chaperoning activities associated with enterovirus 2CATPase, and our study provides both in vitro and cellular evidence for their potential roles during viral RNA replication. These findings increase our

  5. The Putative Son's Attractiveness Alters the Perceived Attractiveness of the Putative Father.

    Science.gov (United States)

    Prokop, Pavol

    2015-08-01

    A body of literature has investigated female mate choice in the pre-mating context (pre-mating sexual selection). Humans, however, are long-living mammals forming pair-bonds which sequentially produce offspring. Post-mating evaluations of a partner's attractiveness may thus significantly influence the reproductive success of men and women. I tested herein the theory that the attractiveness of putative sons provides extra information about the genetic quality of fathers, thereby influencing fathers' attractiveness across three studies. As predicted, facially attractive boys were more frequently attributed to attractive putative fathers and vice versa (Study 1). Furthermore, priming with an attractive putative son increased the attractiveness of the putative father with the reverse being true for unattractive putative sons. When putative fathers were presented as stepfathers, the effect of the boy's attractiveness on the stepfather's attractiveness was lower and less consistent (Study 2). This suggests that the presence of an attractive boy has the strongest effect on the perceived attractiveness of putative fathers rather than on non-fathers. The generalized effect of priming with beautiful non-human objects also exists, but its effect is much weaker compared with the effects of putative biological sons (Study 3). Overall, this study highlighted the importance of post-mating sexual selection in humans and suggests that the heritable attractive traits of men are also evaluated by females after mating and/or may be used by females in mate poaching.

  6. Elevated CO2 concentration around alfalfa nodules increases N2 fixation

    OpenAIRE

    Fischinger, Stephanie A.; Hristozkova, Marieta; Mainassara, Zaman-Allah; Schulze, Joachim

    2009-01-01

    Nodule CO2 fixation via PEPC provides malate for bacteroids and oxaloacetate for N assimilation. The process is therefore of central importance for efficient nitrogen fixation. Nodule CO2 fixation is known to depend on external CO2 concentration. The hypothesis of the present paper was that nitrogen fixation in alfalfa plants is enhanced when the nodules are exposed to elevated CO2 concentrations. Therefore nodulated plants of alfalfa were grown in a hydroponic system that allowed separate ae...

  7. The Role of Proanthocyanidins Complex in Structure and Nutrition Interaction in Alfalfa Forage

    OpenAIRE

    Jonker, Arjan; Yu, Peiqiang

    2016-01-01

    Alfalfa (Medicago sativa L.) is one of the main forages grown in the world. Alfalfa is a winter hardy, drought tolerant, N-fixing legume with a good longevity, high yield, high nutrient levels, high digestibility, unique structural to non-structural components ratio, high dry matter intake, and high animal productivity per hectare. However, its main limitation is its excessively rapid initial rate of protein degradation in the rumen, which results in pasture bloat and inefficient use of prote...

  8. The effects of alfalfa particle size and acid treated protein on ruminal ...

    African Journals Online (AJOL)

    DR. NJ TONUKARI

    2011-10-17

    Oct 17, 2011 ... received a mixed diet (% of dry matter) consisting of 23.73 alfalfa, 8.70 canola meal, 39.56 wheat straw,. 13.45 beet pulp and 13.45 ... ruminal mean retention time of plastic particles in sheep. (Kaske and Engelhardt .... 13.45 and 13.45% of alfalfa forage, canola meal, wheat straw, beet pulp and barley grain, ...

  9. Proteomic identification of differentially expressed proteins during alfalfa (Medicago sativa L. flower development

    Directory of Open Access Journals (Sweden)

    Lingling Chen

    2016-10-01

    Full Text Available Flower development, pollination, and fertilization are important stages in the sexual reproduction process of plants; they are also critical steps in the control of seed formation and development. During alfalfa (Medicago sativa L. seed production, some distinct phenomena such as a low seed setting ratio, serious flower falling, and seed abortion commonly occur. However, the causes of these phenomena are complicated and largely unknown. An understanding of the mechanisms that regulate alfalfa flowering is important in order to increase seed yield. Hence, proteomic technology was used to analyze changes in protein expression during the stages of alfalfa flower development. Flower samples were collected at pre-pollination (S1, pollination (S2, and the post-pollination senescence period (S3. Twenty-four differentially expressed proteins were successfully identified, including 17 down-regulated in pollinated flowers, one up-regulated in pollinated and senesced flowers, and six up-regulated in senesced flowers. The largest proportions of the identified proteins were involved in metabolism, signal transduction, defense response, oxidation reduction, cell death, and programmed cell death (PCD. Their expression profiles demonstrated that energy metabolism, carbohydrate metabolism, and amino acid metabolism provided the nutrient foundation for pollination in alfalfa. Furthermore, there were three proteins involved in multiple metabolic pathways: dual specificity kinase splA-like protein (kinase splALs, carbonic anhydrase (CA, and NADPH: quinone oxidoreductase-like protein (NQOLs. Expression patterns of these proteins indicated that MAPK cascades regulated multiple processes, such as signal transduction, stress response, and cell death. PCD also played an important role in the alfalfa flower developmental process, and regulated both pollination and flower senescence. The current study sheds some light on protein expression profiles during alfalfa flower

  10. Nitrogen replacement value of alfalfa to corn and wheat under irrigated Mediterranean conditions

    OpenAIRE

    Ballesta, A.; Lloveras, J.

    2010-01-01

    In crop rotations that include alfalfa (Medicago sativa L.), agronomic and environmental concerns mean that it is important to determine the N fertilizer contribution of this legume for subsequent crops in order to help to increase the sustainability of cropping systems. To determine the N fertilizer replacement value (FRV) of a 2-yr alfalfa crop on subsequent crops of corn (Zea mays L.) followed by wheat (Triticum aestivum L.) under irrigated Mediterranean conditions, two 4-yr rotations (alf...

  11. Proteomic Identification of Differentially Expressed Proteins during Alfalfa (Medicago sativa L.) Flower Development.

    Science.gov (United States)

    Chen, Lingling; Chen, Quanzhu; Zhu, Yanqiao; Hou, Longyu; Mao, Peisheng

    2016-01-01

    Flower development, pollination, and fertilization are important stages in the sexual reproduction process of plants; they are also critical steps in the control of seed formation and development. During alfalfa ( Medicago sativa L.) seed production, some distinct phenomena such as a low seed setting ratio, serious flower falling, and seed abortion commonly occur. However, the causes of these phenomena are complicated and largely unknown. An understanding of the mechanisms that regulate alfalfa flowering is important in order to increase seed yield. Hence, proteomic technology was used to analyze changes in protein expression during the stages of alfalfa flower development. Flower samples were collected at pre-pollination (S1), pollination (S2), and the post-pollination senescence period (S3). Twenty-four differentially expressed proteins were successfully identified, including 17 down-regulated in pollinated flowers, one up-regulated in pollinated and senesced flowers, and six up-regulated in senesced flowers. The largest proportions of the identified proteins were involved in metabolism, signal transduction, defense response, oxidation reduction, cell death, and programmed cell death (PCD). Their expression profiles demonstrated that energy metabolism, carbohydrate metabolism, and amino acid metabolism provided the nutrient foundation for pollination in alfalfa. Furthermore, there were three proteins involved in multiple metabolic pathways: dual specificity kinase splA-like protein (kinase splALs), carbonic anhydrase, and NADPH: quinone oxidoreductase-like protein. Expression patterns of these proteins indicated that MAPK cascades regulated multiple processes, such as signal transduction, stress response, and cell death. PCD also played an important role in the alfalfa flower developmental process, and regulated both pollination and flower senescence. The current study sheds some light on protein expression profiles during alfalfa flower development and

  12. X-ray structure of the pestivirus NS3 helicase and its conformation in solution.

    Science.gov (United States)

    Tortorici, M Alejandra; Duquerroy, Stéphane; Kwok, Jane; Vonrhein, Clemens; Perez, Javier; Lamp, Benjamin; Bricogne, Gerard; Rümenapf, Till; Vachette, Patrice; Rey, Félix A

    2015-04-01

    Pestiviruses form a genus in the Flaviviridae family of small enveloped viruses with a positive-sense single-stranded RNA genome. Viral replication in this family requires the activity of a superfamily 2 RNA helicase contained in the C-terminal domain of nonstructural protein 3 (NS3). NS3 features two conserved RecA-like domains (D1 and D2) with ATPase activity, plus a third domain (D3) that is important for unwinding nucleic acid duplexes. We report here the X-ray structure of the pestivirus NS3 helicase domain (pNS3h) at a 2.5-Å resolution. The structure deviates significantly from that of NS3 of other genera in the Flaviviridae family in D3, as it contains two important insertions that result in a narrower nucleic acid binding groove. We also show that mutations in pNS3h that rescue viruses from which the core protein is deleted map to D3, suggesting that this domain may be involved in interactions that facilitate particle assembly. Finally, structural comparisons of the enzyme in different crystalline environments, together with the findings of small-angle X-ray-scattering studies in solution, show that D2 is mobile with respect to the rest of the enzyme, oscillating between closed and open conformations. Binding of a nonhydrolyzable ATP analog locks pNS3h in a conformation that is more compact than the closest apo-form in our crystals. Together, our results provide new insight and bring up new questions about pNS3h function during pestivirus replication. Although pestivirus infections impose an important toll on the livestock industry worldwide, little information is available about the nonstructural proteins essential for viral replication, such as the NS3 helicase. We provide here a comparative structural and functional analysis of pNS3h with respect to its orthologs in other viruses of the same family, the flaviviruses and hepatitis C virus. Our studies reveal differences in the nucleic acid binding groove that could have implications for understanding the

  13. Radiation balance of an alfalfa crop in Saudi Arabia

    International Nuclear Information System (INIS)

    Al-Yemeni, M.N.; Grace, J.

    1995-01-01

    Short-wave reflectivity or albedo is an important component of net radiation which represents the major determinant of radiation balance of crop surface. This study was conducted on an irrigated alfalfa crop field at Al-Kharj agricultural area in Saudi Arabia, grown according to normal agricultural practices. Data on radiation balance and crop cover were collected over a number of days from March to October 1986, crop albedo varying from 0–4 in early morning to 0–20 at noon, the overall mean value of the crop albedo being estimated at 0–26. The relation between the individual components of radiation balance was studied, and a significant correlation between incident radiation and net radiation was found. Possible causes responsible for changes in crop albedo were discussed. (author)

  14. Resistant and susceptible responses in alfalfa (Medicago sativa to bacterial stem blight caused by Pseudomonas syringae pv. syringae.

    Directory of Open Access Journals (Sweden)

    Lev G Nemchinov

    Full Text Available Bacterial stem blight caused by Pseudomonas syringae pv. syringae is a common disease of alfalfa (Medicago sativa L. Little is known about host-pathogen interactions and host defense mechanisms. Here, individual resistant and susceptible plants were selected from cultivars Maverick and ZG9830 and used for transcript profiling at 24 and 72 hours after inoculation (hai with the isolate PssALF3. Bioinformatic analysis revealed a number of differentially expressed genes (DEGs in resistant and susceptible genotypes. Although resistant plants from each cultivar produced a hypersensitive response, transcriptome analyses indicated that they respond differently at the molecular level. The number of DEGs was higher in resistant plants of ZG9830 at 24 hai than in Maverick, suggesting that ZG9830 plants had a more rapid effector triggered immune response. Unique up-regulated genes in resistant ZG9830 plants included genes encoding putative nematode resistance HSPRO2-like proteins, orthologs for the rice Xa21 and soybean Rpg1-b resistance genes, and TIR-containing R genes lacking both NBS and LRR domains. The suite of R genes up-regulated in resistant Maverick plants had an over-representation of R genes in the CC-NBS-LRR family including two genes for atypical CCR domains and a putative ortholog of the Arabidopsis RPM1 gene. Resistance in both cultivars appears to be mediated primarily by WRKY family transcription factors and expression of genes involved in protein phosphorylation, regulation of transcription, defense response including synthesis of isoflavonoids, and oxidation-reduction processes. These results will further the identification of mechanisms involved in resistance to facilitate selection of parent populations and development of commercial varieties.

  15. Alfalfa root role in osmotic adjustment under salt stress (abstract)

    International Nuclear Information System (INIS)

    Ibriz, M.; Ghorri, M.; Alami, T.; El Guilli, M.; El- Moidaoui, M.; Benbella, M.

    2005-01-01

    The aim of this work was to evaluate the effect of the sodium chloride on the morpho physiological characteristics of Alfalfa (Medicago sativa L.). The characteristics taken into consideration dry matter production of shoot and root (DMS, DMR), root volume (RV), proline content (PS, PR), included total soluble sugar (SSS; SSR) and chlorophyll a, band (a+b). Salt tolerance of the six genotypes was characterised by capacity to growth in salt environment, buildup of osmoregulating compounds (proline and solubles sugar) and a less inhibition of photosynthesis process (decrease of chlorophyll pigment content). Important genotypes differences were observed for each parameter, which make possible a better understanding of the Alfalfa adaptation mechanisms. The results show that the salt stress has a significant influence on the growth of this plants by decreasing the production of dry matter and :)f the root volume. The most important decreases were clear at the 12 g/l concentration mainly upon the Australian variety (Siriver).Thus the most tolerant to salt stress was the Demnate genotype (Dem04) which presented the lowest decrease percentage. The salt effect upon the plant physiological characteristics causes a decrease of the relative water content and chlorophyll a, b and (a+b) content. It also causes an increase of the relative loss of water, the total soluble sugars (SSS; SSR) and the proline contents (PS, PR). Thus, we found a high correlation between the proline and sugar contents of shoot and root and also between these substances and shoot and root dry matter production. (author)

  16. Alimentos funcionales, alfalfa y fitoestrógenos

    Directory of Open Access Journals (Sweden)

    Alejandro De Jesús

    2016-05-01

    Full Text Available El desarrollo de alimentos funcionales en los últimos años ha ido en aumento debido principalmente, al interés de la población por alimentos que no solo cumplan con la función nutricional sino también por que tengan un efecto benéfico en salud reduciendo así el riesgo a padecer diversas enfermedades. La alfalfa ha sido generalmente un alimento destinado para la alimentación del ganado, sin embargo, en diversas investigaciones alrededor del mundo se ha reportado que contiene compuestos bioactivos –fitoquímicos– y proteínas con efecto estrogénico, antimicrobiano y antioxidante, así como también protector contra enfermedades cardiovasculares, cáncer y diabetes, entre otras, clasificándola potencialmente como un alimento funcional. El presente documento tiene como objetivo dar un bosquejo general informativo a través de la búsqueda y revisión bibliográfica acerca de los alimentos funcionales y en especial de la alfalfa y constituyentes fitoquímicos (fitoestrógenos que la ubican dentro de este grupo de alimentos; así como los hallazgos que se han reportado como efectos adversos en animales experimentales específicamente en el aparato reproductivo debido al consumo de este tipo de fitocompuestos. Esta dicotomía entre los efectos adversos y benéficos no es más que la señalización de que aún falta mucha más información y estudios que realizar respecto al resultado que pueden tener los fitoestrógenos en el desarrollo y función reproductiva de animales, el agonismo y antagonismo de su efecto así como la concordancia en el riesgo-beneficio de su consumo.

  17. The Baryonic Tully Fisher Relation for the ALFALFA 100 Sample

    Science.gov (United States)

    Finney, Elizabeth E.; Haynes, Martha P.; APPSS Team

    2018-01-01

    The APPSS (Arecibo Pisces-Perseus Supercluster Survey) team aims to quantify the over-densities of matter in the Pisces-Perseus Supercluster (PPS) filament by exploring the Baryonic Tully Fisher Relation (BTFR) of the ALFALFA (Arecibo Legacy Fast ALFA) 100 survey – (α.100) and, in the future, using targeted observations of low mass star-forming galaxies. Galaxies in the PPS filament region and its foreground and background voids are influenced by the gravitational pull of the large concentration of matter, and are expected to show velocities that deviate significantly from the smooth Hubble expansion. By deriving the peculiar motions of galaxies in the ALFALFA 100 survey as measured by the BTFR, we will further our understanding of the amount and distribution of the underlying dark matter in the supercluster. In this project, we make a first attempt to investigate the BTFR of the α.100 sample, and discuss our findings. This sample was corrected for inclination, extinction, and other sources of scatter, and a least squares linear regression fit was applied to determine the slope of the BTFR. We compare the slope of the α.100 sample to various literature values, and find that the slope is shallower due to slower-rotating, low-mass galaxies. Investigation of this shallow slope is needed in future work, as well as a modification of the intrinsic axial ratio assumed for this sample of galaxies. EF participated in the summer 2017 REU program in the Center for Astrophysics and Planetary Science at Cornell University under NSF award AST-1659264.

  18. Study on the reduction and hysteresis effect of soil nitrogen pollution by Alfalfa in channel buffer bank

    Science.gov (United States)

    Chi, Yixia; Xue, Lianqing; Zhang, Zhanyu; Li, Dongying

    2018-01-01

    Based on the simulation experiments of solute transport in channel buffer bank and pot experiments, this study analyzed the transport of nitrogen pollution from farmland drains along the South-North Water Transfer east route project; and compared the nitrogen transport rule and purification effect of alfalfa in channel buffer bank soil under situations of bare land and alfalfa mulching. The results showed that: (1) soil nitrogen content decreased gradually with the width increase of channel buffer bank by the soil adsorption and decomposition; (2) the migration rates of nitrogen were 0.06 g·kg-1 by the alfalfa mulching; (3) the removed rates of nitrogen from the soil were 0.088 g·kg-1 by cutting alfalfa; (4) the residual nitrogen of soil with alfalfa was 10% of the bare land. Alfalfa in channel buffer bank had obvious reduction and hysteresis effect to soil nitrogen pollution.

  19. Effectiveness of neutral detergent fiber in whole cottonseed and dried distillers grains compared with alfalfa haylage.

    Science.gov (United States)

    Clark, P W; Armentano, L E

    1993-09-01

    Sixteen Holstein cows in midlactation were used in a 4 x 4 Latin square design to determine the effect of replacing alfalfa NDF with NDF from whole, linted cottonseed or dried distillers grains. Low and high fiber control diets (13 and 19% of dietary DM from alfalfa haylage NDF, respectively) were compared with diets designed to contain 13% of DM from alfalfa haylage NDF plus 6% of DM from either cottonseed NDF or distillers grains NDF. Dry matter intake, milk yield, and milk protein yield were lower from the high fiber control diet. Milk fat percentage was lower for the low fiber control diet. The cottonseed diet was equal to the high fiber control diet in stimulating rumination. Rumen acetate to propionate ratio was higher for the high fiber control and cottonseed diets. Replacing alfalfa with either of these high fiber by-product feeds increased feed intake and yields of milk fat and protein. The effectiveness of the NDF in distillers grains and cottonseed was not significantly different from that of alfalfa NDF for maintaining milk fat yield. Whole cottonseed and dried distillers grains appear to be good sources of effective fiber for maintaining milk fat test when they are substituted for alfalfa haylage fiber in lactating cow rations.

  20. Application of corn meal at ensiling of alfalfa cocksfoot and their mixture

    Directory of Open Access Journals (Sweden)

    Knežević Jasmin A.

    2014-01-01

    Full Text Available One of the solutions for the economical use of alfalfa and cocksfoot is making the silage. However, these plant species are difficult to be conserved without appropriate additives. The aim of this study was to determine the impact addition of cornmeal on the quality of silage of alfalfa (Medicago sativa L. cv. Kruševačka 22, cocksfoot (Dactilys glomerata L. cv. Kruševačka 40 and their mixture (50% alfalfa, 50% cocksfoot. Mowing both species was carried out at the stage when 1/3 to 1/5 of the plants were in flowering in alfalfa or in stage appearance of inflorescence with cocksfoot. Corn grain is ground at the mill with a sieve ø 2 mm, then mixed with chopped fodder of alfalfa, cocksfoot and the mixture in the following amount: 6% (treatment A2, 3% (treatment A1, and without cornmeal addition (control A0. After six months was determined silage quality. Cornmeal addition, according to the basic indicators of the quality of silage had a significant impact on changing the quality silage of alfalfa, cocksfoot and their mixtures. It is evident that the addition cornmeal addition a significant impact on increasing the energy value (primarily the content inside BEM of silage in all studied treatments.

  1. [Determination of Hard Rate of Alfalfa (Medicago sativa L.) Seeds with Near Infrared Spectroscopy].

    Science.gov (United States)

    Wang, Xin-xun; Chen, Ling-ling; Zhang, Yun-wei; Mao, Pei-sheng

    2016-03-01

    Alfalfa (Medicago sativa L.) is the most commonly grown forage crop due to its better quality characteristics and high adaptability in China. However, there was 20%-80% hard seeds in alfalfa which could not be identified easily from non hard seeds which would cause the loss of seed utilization value and plant production. This experiment was designed for 121 samples of alfalfa. Seeds were collected according to different regions, harvested year and varieties. 31 samples were artificial matched as hard rates ranging from 20% to 80% to establish a model for hard seed rate by near infrared spectroscopy (NIRS) with Partial Least Square (PLS). The objective of this study was to establish a model and to estimate the efficiency of NIRS for determining hard rate of alfalfa seeds. The results showed that the correlation coefficient (R2(cal)) of calibration model was 0.981 6, root mean square error of cross validation (RMSECV) was 5.32, and the ratio of prediction to deviation (RPD) was 3.58. The forecast model in this experiment presented the satisfied precision. The proposed method using NIRS technology is feasible for identification and classification of hard seed in alfalfa. A new method, as nondestructive testing of hard seed rate, was provided to theoretical basis for fast nondestructive detection of hard seed rates in alfalfa.

  2. EM structure of a helicase-loader complex depicting a 6:2 binding sub-stoichiometry from Geobacillus kaustophilus HTA426

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Yen-Chen [Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan (China); Naveen, Vankadari [Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan (China); Molecular Cell Biology, Taiwan International Graduate Program, Institute of Molecular Biology, Academia Sinica, and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan (China); Hsiao, Chwan-Deng, E-mail: hsiao@gate.sinica.edu.tw [Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan (China); Molecular Cell Biology, Taiwan International Graduate Program, Institute of Molecular Biology, Academia Sinica, and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan (China)

    2016-04-22

    During DNA replication, bacterial helicase is recruited as a complex in association with loader proteins to unwind the parental duplex. Previous structural studies have reported saturated 6:6 helicase-loader complexes with different conformations. However, structural information on the sub-stoichiometric conformations of these previously-documented helicase-loader complexes remains elusive. Here, with the aid of single particle electron-microscopy (EM) image reconstruction, we present the Geobacillus kaustophilus HTA426 helicase-loader (DnaC-DnaI) complex with a 6:2 binding stoichiometry in the presence of ATPγS. In the 19 Å resolution EM map, the undistorted and unopened helicase ring holds a robust loader density above the C-terminal RecA-like domain. Meanwhile, the path of the central DNA binding channel appears to be obstructed by the reconstructed loader density, implying its potential role as a checkpoint conformation to prevent the loading of immature complex onto DNA. Our data also reveals that the bound nucleotides and the consequently induced conformational changes in the helicase hexamer are essential for active association with loader proteins. These observations provide fundamental insights into the formation of the helicase-loader complex in bacteria that regulates the DNA replication process. - Highlights: • Helicase-loader complex structure with 6:2 sub-stoichiometry is resolved by EM. • Helicase hexamer in 6:2 sub-stoichiometry is constricted and un-opened. • 6:2 binding ratio of helicase-loader complex could act as a DNA loading checkpoint. • Nucleotides stabilize helicase-loader complex at low protein concentrations.

  3. EM structure of a helicase-loader complex depicting a 6:2 binding sub-stoichiometry from Geobacillus kaustophilus HTA426

    International Nuclear Information System (INIS)

    Lin, Yen-Chen; Naveen, Vankadari; Hsiao, Chwan-Deng

    2016-01-01

    During DNA replication, bacterial helicase is recruited as a complex in association with loader proteins to unwind the parental duplex. Previous structural studies have reported saturated 6:6 helicase-loader complexes with different conformations. However, structural information on the sub-stoichiometric conformations of these previously-documented helicase-loader complexes remains elusive. Here, with the aid of single particle electron-microscopy (EM) image reconstruction, we present the Geobacillus kaustophilus HTA426 helicase-loader (DnaC-DnaI) complex with a 6:2 binding stoichiometry in the presence of ATPγS. In the 19 Å resolution EM map, the undistorted and unopened helicase ring holds a robust loader density above the C-terminal RecA-like domain. Meanwhile, the path of the central DNA binding channel appears to be obstructed by the reconstructed loader density, implying its potential role as a checkpoint conformation to prevent the loading of immature complex onto DNA. Our data also reveals that the bound nucleotides and the consequently induced conformational changes in the helicase hexamer are essential for active association with loader proteins. These observations provide fundamental insights into the formation of the helicase-loader complex in bacteria that regulates the DNA replication process. - Highlights: • Helicase-loader complex structure with 6:2 sub-stoichiometry is resolved by EM. • Helicase hexamer in 6:2 sub-stoichiometry is constricted and un-opened. • 6:2 binding ratio of helicase-loader complex could act as a DNA loading checkpoint. • Nucleotides stabilize helicase-loader complex at low protein concentrations.

  4. El cultivo de alfalfa utilizando agua de perforación, agua residual urbana y precipitaciones The cultivation of alfalfa using artesian well water, urban wastewater and rainfall

    Directory of Open Access Journals (Sweden)

    José O. Plevich

    2012-12-01

    Full Text Available El objetivo de este trabajo fue analizar la producción de biomasa aérea, la eficiencia del uso de agua y el valor nutritivo de alfalfa cultivada aplicando riego con agua residual urbana, agua de perforación y un testigo (precipitaciones, en el Campus de la Universidad Nacional de Rio Cuarto (Córdoba-Argentina. Los tratamientos de riego tuvieron un efecto positivo sobre la producción de biomasa aérea obteniéndose un 24% más de producción de biomasa que en la situación de secano (precipitaciones. Entre los tratamientos con riego también se manifestaron diferencias estadísticamente significativas. La alfalfa regada con aguas residuales urbana supero en un 19% a la cultivada con agua de perforación. La eficiencia del uso del agua por parte del cultivo se incrementó cuando el riego se realizó con aguas residuales urbanas. Además, se determinó que la alfalfa regada con agua residual, supera los valores nutritivos del cultivo que crece en condiciones sin riego; encontrándose 39% más de proteínas, 14% más de digestibilidad e igual porcentaje de energía metabólica. Se puede concluir que el agua residual urbana representa otra posible fuente de agua, factible de ingresar al suelo y estar a disposición para el cultivo de alfalfa.The objective of this study was to analyse the production of alfalfa biomass, the efficiency of water use and the nutritional value of forage, inside an irrigation structure of an experimental facility that uses treated urban wastewater, artesian well water and rainfall, at the campus of the Universidad National de Rio Cuarto (Córdoba-Argentina. The irrigation treatment had a positive effect on the production of biomass of alfalfa. On an average 24% increase in production was observed when compared to dry-land farming. Regarding the quality of the irrigation water, statistical differences in production were observed, the irrigation with urban wastewater produced 19% more than that of well water. The

  5. Interactive Roles of DNA Helicases and Translocases with the Single-Stranded DNA Binding Protein RPA in Nucleic Acid Metabolism.

    Science.gov (United States)

    Awate, Sanket; Brosh, Robert M

    2017-06-08

    Helicases and translocases use the energy of nucleoside triphosphate binding and hydrolysis to unwind/resolve structured nucleic acids or move along a single-stranded or double-stranded polynucleotide chain, respectively. These molecular motors facilitate a variety of transactions including replication, DNA repair, recombination, and transcription. A key partner of eukaryotic DNA helicases/translocases is the single-stranded DNA binding protein Replication Protein A (RPA). Biochemical, genetic, and cell biological assays have demonstrated that RPA interacts with these human molecular motors physically and functionally, and their association is enriched in cells undergoing replication stress. The roles of DNA helicases/translocases are orchestrated with RPA in pathways of nucleic acid metabolism. RPA stimulates helicase-catalyzed DNA unwinding, enlists translocases to sites of action, and modulates their activities in DNA repair, fork remodeling, checkpoint activation, and telomere maintenance. The dynamic interplay between DNA helicases/translocases and RPA is just beginning to be understood at the molecular and cellular levels, and there is still much to be learned, which may inform potential therapeutic strategies.

  6. Identification and characterization of putative conserved IAM ...

    African Journals Online (AJOL)

    Available putative AMI sequences from a wide array of monocot and dicot plants were identified and the phylogenetic tree was constructed and analyzed. We identified in this tree, a clade that contained sequences from species across the plant kingdom suggesting that AMI is conserved and may have a primary role in plant ...

  7. Toddlers' Duration of Attention toward Putative Threat

    Science.gov (United States)

    Kiel, Elizabeth J.; Buss, Kristin A.

    2011-01-01

    Although individual differences in reactions to novelty in the toddler years have been consistently linked to risk of developing anxious behavior, toddlers' attention toward a novel, putatively threatening stimulus while in the presence of other enjoyable activities has rarely been examined as a precursor to such risk. The current study examined…

  8. Role of the ATPase/helicase maleless (MLE in the assembly, targeting, spreading and function of the male-specific lethal (MSL complex of Drosophila

    Directory of Open Access Journals (Sweden)

    Morra Rosa

    2011-04-01

    Full Text Available Abstract Background The male-specific lethal (MSL complex of Drosophila remodels the chromatin of the X chromosome in males to enhance the level of transcription of most X-linked genes, and thereby achieve dosage compensation. The core complex consists of five proteins and one of two non-coding RNAs. One of the proteins, MOF (males absent on the first, is a histone acetyltransferase that specifically acetylates histone H4 at lysine 16. Another protein, maleless (MLE, is an ATP-dependent helicase with the ability to unwind DNA/RNA or RNA/RNA substrates in vitro. Recently, we showed that the ATPase activity of MLE is sufficient for the hypertranscription of genes adjacent to a high-affinity site by MSL complexes located at that site. The helicase activity is required for the spreading of the complex to the hundreds of positions along the X chromosome, where it is normally found. In this study, to further understand the role of MLE in the function of the MSL complex, we analyzed its relationship to the other complex components by creating a series of deletions or mutations in its putative functional domains, and testing their effect on the distribution and function of the complex in vivo. Results The presence of the RB2 RNA-binding domain is necessary for the association of the MSL3 protein with the other complex subunits. In its absence, the activity of the MOF subunit was compromised, and the complex failed to acetylate histone H4 at lysine 16. Deletion of the RB1 RNA-binding domain resulted in complexes that maintained substantial acetylation activity but failed to spread beyond the high-affinity sites. Flies bearing this mutation exhibited low levels of roX RNAs, indicating that these RNAs failed to associate with the proteins of the complex and were degraded, or that MLE contributes to their synthesis. Deletion of the glycine-rich C-terminal region, which contains a nuclear localization sequence, caused a substantial level of retention of the

  9. Emerging Importance of Helicases in Plant Stress Tolerance: Characterization of Oryza sativa Repair Helicase XPB2 Promoter and Its Functional Validation in Tobacco under Multiple Stresses.

    Science.gov (United States)

    Raikwar, Shailendra; Srivastava, Vineet K; Gill, Sarvajeet S; Tuteja, Renu; Tuteja, Narendra

    2015-01-01

    Genetic material always remains at the risk of spontaneous or induced damage which challenges the normal functioning of DNA molecule, thus, DNA repair is vital to protect the organisms against genetic damage. Helicases, the unique molecular motors, are emerged as prospective molecules to engineer stress tolerance in plants and are involved in nucleic acid metabolism including DNA repair. The repair helicase, XPB is an evolutionary conserved protein present in different organisms, including plants. Availability of few efficient promoters for gene expression in plants provoked us to study the promoter of XPB for better understanding of gene regulation under stress conditions. Here, we report the in silico analysis of novel stress inducible promoter of Oryza sativa XPB2 (OsXPB2). The in vivo validation of functionality/activity of OsXPB2 promoter under abiotic and hormonal stress conditions was performed by Agrobacterium-mediated transient assay in tobacco leaves using OsXPB2::GUS chimeric construct. The present research revealed that OsXPB2 promoter contains cis-elements accounting for various abiotic stresses (salt, dehydration, or cold) and hormone (Auxin, ABA, or MeJA) induced GUS expression/activity in the promoter-reporter assay. The promoter region of OsXPB2 contains CACG, GTAACG, CACGTG, CGTCA CCGCCGCGCT cis acting-elements which are reported to be salt, dehydration, cold, MeJA, or ABA responsive, respectively. Functional analysis was done by Agrobacterium-mediated transient assay using agroinfiltration in tobacco leaves, followed by GUS staining and fluorescence quantitative analyses. The results revealed high induction of GUS activity under multiple abiotic stresses as compared to mock treated control. The present findings suggest that OsXPB2 promoter is a multi-stress inducible promoter and has potential applications in sustainable crop production under abiotic stresses by regulating desirable pattern of gene expression.

  10. Conserved helicase domain of human RecQ4 is required for strand annealing-independent DNA unwinding

    DEFF Research Database (Denmark)

    Rossi, Marie L; Ghosh, Avik K; Kulikowicz, Tomasz

    2010-01-01

    Humans have five members of the well conserved RecQ helicase family: RecQ1, Bloom syndrome protein (BLM), Werner syndrome protein (WRN), RecQ4, and RecQ5, which are all known for their roles in maintaining genome stability. BLM, WRN, and RecQ4 are associated with premature aging and cancer...... provide the first evidence that human RecQ4's unwinding is independent of strand annealing, and that it does not require the presence of excess ssDNA. Moreover, we demonstrate that a point mutation of the conserved lysine in the Walker A motif abolished helicase activity, implying that not the N...... activities and protein partners of RecQ4 are conserved with those of the other RecQ helicases....

  11. Screening of Cd tolerant genotypes and isolation of metallothionein genes in alfalfa (Medicago sativa L.)

    International Nuclear Information System (INIS)

    Wang Xiaojuan; Song, Yu; Ma Yanhua; Zhuo Renying; Jin Liang

    2011-01-01

    In order to evaluate Cd tolerance in wide-ranging sources of alfalfa (Medicago sativa) and to identify Cd tolerant genotypes which may potentially be useful for restoring Cd-contaminated environments, thirty-six accessions of alfalfa were screened under hydroponic culture. Our results showed that the relative root growth rate varied from 0.48 to 1.0, which indicated that different alfalfa accessions had various responses to Cd stress. The candidate fragments derived from differentially expressed metallothionein (MT) genes were cloned from leaves of two Cd tolerant genotypes, YE and LZ. DNA sequence and the deduced protein sequence showed that MsMT2a and MsMT2b had high similarity to those in leguminous plants. DDRT-PCR analysis showed that MsMT2a expressed in both YE and LZ plants under control and Cd stress treatment, but MsMT2b only expressed under Cd stress treatment. This suggested that MsMT2a was universally expressed in leaves of alfalfa but expression of MsMT2b was Cadmium (Cd) inducible. - Highlights: → Evaluate Cd tolerance in wide sources of alfalfa accessions. → Identify Cd-hyperaccumulators potentially useful for restoring Cd-contaminated environments. → Cloned differentially expressed metallothionein (MT) genes. → Characteristics and deduced protein sequence of MsMT2a and MsMT2b were analyzed. → MsMT2a might be a universally gene of alfalfa but MsMT2b might be an inductive gene. - Two Cd tolerant alfalfa genotypes were screened and their metallothionein genes were cloned which showed that MsMT2a was universally expressed but MsMT2b was Cd inducible expression.

  12. Effects of dietary alfalfa inclusion on Salmonella typhimurium populations in growing layer chicks.

    Science.gov (United States)

    Escarcha, Jacquelyn F; Callaway, Todd R; Byrd, J Allen; Miller, Dan N; Edrington, Tom S; Anderson, Robin C; Nisbet, David J

    2012-10-01

    Reducing Salmonella in poultry has been a paramount goal of the poultry industry in order to improve food safety. Inclusion of high-fiber fermentable feedstuffs in chicken diets has been shown to reduce the incidence of Salmonella colonization in laying hens, but no work has been performed in growing birds. Therefore, the present study was designed to quantify differences in artificially inoculated cecal Salmonella Typhimurium populations in growing layer chicks (n = 60 in each of two replications) fed 0%, 25%, and 50% of their diet (w/w) replaced with alfalfa meal from day (d) 7 to d14 after hatch. Alfalfa supplementation reduced cecal populations of Salmonella by 0.95 and 1.25 log10 colony-forming unit per gram in the 25% and 50% alfalfa groups compared to controls. Alfalfa feeding reduced (p < 0.05) the number of cecal- and crop-positive birds compared to controls. Increasing levels of alfalfa increased (p < 0.05) total volatile fatty acids (VFA) and the proportion of acetate in the cecum. Surprisingly, alfalfa inclusion did not negatively impact average daily gain (ADG) in birds over the 7-d feeding period. Alfalfa inclusion at 50% of the diet increased (p < 0.05) the number of bacterial genera detected in the cecum compared to controls, and also altered proportions of the microbial population by reducing Ruminococcus and increasing Clostridia populations. Results support the idea that providing a fermentable substrate can increase gastrointestinal VFA production and bacterial diversity which in turn can reduce colonization by Salmonella via natural competitive barriers. However, further studies are obviously needed to more fully understand the impact of changes made in diet or management procedures on poultry production.

  13. Effectivenes of inoculation in alfalfa breeding in ecological conditions of the Bjelovar and Bilogora county

    Directory of Open Access Journals (Sweden)

    Darko Uher

    2012-09-01

    Full Text Available Development and basic existence of animal production as well as production of high quality milk depends upon possibility of sufficient production of quality and protein sufficient forage. Forage crop that satisfies these demands is alfalfa which is one of the most important perennial forage crop legumes. The aim of this study was to enhance alfalfa production on acid soil by liming and alfalfa seed inoculation with efficient Sinorhizobium meliloti strains in order to reduce the use of mineral nitrogen fertilization and enable qualitative and cost effective production of forage on the dairy farms. Field trial was established at family farm in the area of Bjelovar and Bilogora county. During two years experimental period statistically significant influence of inoculation and liming on forage and dry matteryield was determined. Significantly the lowest yields were determined on untreated plots without liming material. In all untreated plots, significantly lower yields were determined, but significant differences in yields were also obtained by inoculation with different S. meliloti strains, emphasizing the importance of strains selection used for alfalfa inoculation. In both experimental years total forage yield were ranging from 34 t/ha (untreated plots without liming up to 60 t/ha on plots inoculated with strain 2011 and without liming. Values of total dry matter yield for both experimental years ranged from 6.5 t/ha (untreated plots without liming up to 15,7 t/ha on plots inoculated with strain 2011 without liming. Results of this study showed that application of liming materials for acidity removal had positive effect on alfalfa yields in both experimental years and significantly improved alfalfa production on acid soils. The results of this study clearly showed that inoculation with selected S. meliloti strains may improve alfalfa production on acid soils and may contribute to more efficient forage production for dairy farms under particular

  14. Screening of Cd tolerant genotypes and isolation of metallothionein genes in alfalfa (Medicago sativa L.)

    Energy Technology Data Exchange (ETDEWEB)

    Wang Xiaojuan, E-mail: xiaojuanwang@lzu.edu.cn [School of Pastoral Agriculture Science and Technology, Lanzhou University, P.O. Box 61, Lanzhou 730020 (China); Song, Yu [School of Pastoral Agriculture Science and Technology, Lanzhou University, P.O. Box 61, Lanzhou 730020 (China); Environment Management College of China, Qinhuangdao 066004 (China); Ma Yanhua [Hebei Normal University of Science and Technology, Qinhuangdao 066004 (China); Zhuo Renying [Key Lab of Tree Genomics, Research Institute of Subtropical of Forest, Chinese Academy of Forest, Fuyang 311400 (China); Jin Liang [School of Pastoral Agriculture Science and Technology, Lanzhou University, P.O. Box 61, Lanzhou 730020 (China)

    2011-12-15

    In order to evaluate Cd tolerance in wide-ranging sources of alfalfa (Medicago sativa) and to identify Cd tolerant genotypes which may potentially be useful for restoring Cd-contaminated environments, thirty-six accessions of alfalfa were screened under hydroponic culture. Our results showed that the relative root growth rate varied from 0.48 to 1.0, which indicated that different alfalfa accessions had various responses to Cd stress. The candidate fragments derived from differentially expressed metallothionein (MT) genes were cloned from leaves of two Cd tolerant genotypes, YE and LZ. DNA sequence and the deduced protein sequence showed that MsMT2a and MsMT2b had high similarity to those in leguminous plants. DDRT-PCR analysis showed that MsMT2a expressed in both YE and LZ plants under control and Cd stress treatment, but MsMT2b only expressed under Cd stress treatment. This suggested that MsMT2a was universally expressed in leaves of alfalfa but expression of MsMT2b was Cadmium (Cd) inducible. - Highlights: > Evaluate Cd tolerance in wide sources of alfalfa accessions. > Identify Cd-hyperaccumulators potentially useful for restoring Cd-contaminated environments. > Cloned differentially expressed metallothionein (MT) genes. > Characteristics and deduced protein sequence of MsMT2a and MsMT2b were analyzed. > MsMT2a might be a universally gene of alfalfa but MsMT2b might be an inductive gene. - Two Cd tolerant alfalfa genotypes were screened and their metallothionein genes were cloned which showed that MsMT2a was universally expressed but MsMT2b was Cd inducible expression.

  15. Transcriptome analysis of resistant and susceptible alfalfa cultivars infected with root-knot nematode Meloidogyne incognita.

    Directory of Open Access Journals (Sweden)

    Olga A Postnikova

    Full Text Available Nematodes are one of the major limiting factors in alfalfa production. Root-knot nematodes (RKN, Meloidogyne spp. are widely distributed and economically important sedentary endoparasites of agricultural crops and they may inflict significant damage to alfalfa fields. As of today, no studies have been published on global gene expression profiling in alfalfa infected with RKN or any other plant parasitic nematode. Very little information is available about molecular mechanisms that contribute to pathogenesis and defense responses in alfalfa against these pests and specifically against RKN. In this work, we performed root transcriptome analysis of resistant (cv. Moapa 69 and susceptible (cv. Lahontan alfalfa cultivars infected with RKN Meloidogyne incognita, widespread root-knot nematode species and a major pest worldwide. A total of 1,701,622,580 pair-end reads were generated on an Illumina Hi-Seq 2000 platform from the roots of both cultivars and assembled into 45,595 and 47,590 transcripts in cvs Moapa 69 and Lahontan, respectively. Bioinformatic analysis revealed a number of common and unique genes that were differentially expressed in susceptible and resistant lines as a result of nematode infection. Although the susceptible cultivar showed a more pronounced defense response to the infection, feeding sites were successfully established in its roots. Characteristically, basal gene expression levels under normal conditions differed between the two cultivars as well, which may confer advantage to one of the genotypes toward resistance to nematodes. Differentially expressed genes were subsequently assigned to known Gene Ontology categories to predict their functional roles and associated biological processes. Real-time PCR validated expression changes in genes arbitrarily selected for experimental confirmation. Candidate genes that contribute to protection against M. incognita in alfalfa were proposed and alfalfa-nematode interactions with

  16. The Q Motif Is Involved in DNA Binding but Not ATP Binding in ChlR1 Helicase.

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    Hao Ding

    Full Text Available Helicases are molecular motors that couple the energy of ATP hydrolysis to the unwinding of structured DNA or RNA and chromatin remodeling. The conversion of energy derived from ATP hydrolysis into unwinding and remodeling is coordinated by seven sequence motifs (I, Ia, II, III, IV, V, and VI. The Q motif, consisting of nine amino acids (GFXXPXPIQ with an invariant glutamine (Q residue, has been identified in some, but not all helicases. Compared to the seven well-recognized conserved helicase motifs, the role of the Q motif is less acknowledged. Mutations in the human ChlR1 (DDX11 gene are associated with a unique genetic disorder known as Warsaw Breakage Syndrome, which is characterized by cellular defects in genome maintenance. To examine the roles of the Q motif in ChlR1 helicase, we performed site directed mutagenesis of glutamine to alanine at residue 23 in the Q motif of ChlR1. ChlR1 recombinant protein was overexpressed and purified from HEK293T cells. ChlR1-Q23A mutant abolished the helicase activity of ChlR1 and displayed reduced DNA binding ability. The mutant showed impaired ATPase activity but normal ATP binding. A thermal shift assay revealed that ChlR1-Q23A has a melting point value similar to ChlR1-WT. Partial proteolysis mapping demonstrated that ChlR1-WT and Q23A have a similar globular structure, although some subtle conformational differences in these two proteins are evident. Finally, we found ChlR1 exists and functions as a monomer in solution, which is different from FANCJ, in which the Q motif is involved in protein dimerization. Taken together, our results suggest that the Q motif is involved in DNA binding but not ATP binding in ChlR1 helicase.

  17. Structural and functional analysis of the human spliceosomal DEAD-box helicase Prp28

    Energy Technology Data Exchange (ETDEWEB)

    Möhlmann, Sina [Georg-August-University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen (Germany); Mathew, Rebecca [Max-Planck-Institute for Biophysical Chemistry, Am Fassberg, 37077 Göttingen (Germany); Neumann, Piotr; Schmitt, Andreas [Georg-August-University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen (Germany); Lührmann, Reinhard [Max-Planck-Institute for Biophysical Chemistry, Am Fassberg, 37077 Göttingen (Germany); Ficner, Ralf, E-mail: rficner@uni-goettingen.de [Georg-August-University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen (Germany)

    2014-06-01

    The crystal structure of the helicase domain of the human spliceosomal DEAD-box protein Prp28 was solved by SAD. The binding of ADP and ATP by Prp28 was studied biochemically and analysed with regard to the crystal structure. The DEAD-box protein Prp28 is essential for pre-mRNA splicing as it plays a key role in the formation of an active spliceosome. Prp28 participates in the release of the U1 snRNP from the 5′-splice site during association of the U5·U4/U6 tri-snRNP, which is a crucial step in the transition from a pre-catalytic spliceosome to an activated spliceosome. Here, it is demonstrated that the purified helicase domain of human Prp28 (hPrp28ΔN) binds ADP, whereas binding of ATP and ATPase activity could not be detected. ATP binding could not be observed for purified full-length hPrp28 either, but within an assembled spliceosomal complex hPrp28 gains ATP-binding activity. In order to understand the structural basis for the ATP-binding deficiency of isolated hPrp28, the crystal structure of hPrp28ΔN was determined at 2.0 Å resolution. In the crystal the helicase domain adopts a wide-open conformation, as the two RecA-like domains are extraordinarily displaced from the productive ATPase conformation. Binding of ATP is hindered by a closed conformation of the P-loop, which occupies the space required for the γ-phosphate of ATP.

  18. In vivo mapping of the functional regions of the DEAD-box helicase Vasa

    Directory of Open Access Journals (Sweden)

    Mehrnoush Dehghani

    2015-03-01

    Full Text Available The maternally expressed Drosophila melanogaster DEAD-box helicase Vasa (Vas is necessary for many cellular and developmental processes, including specification of primordial germ cells (pole cells, posterior patterning of the embryo, piRNA-mediated repression of transposon-encoded mRNAs, translational activation of gurken (grk mRNA, and completion of oogenesis itself. Vas protein accumulates in the perinuclear nuage in nurse cells soon after their specification, and then at stage 10 Vas translocates to the posterior pole plasm of the oocyte. We produced a series of transgenic constructs encoding eGFP-Vas proteins carrying mutations affecting different regions of the protein, and analyzed in vivo which Vas functions each could support. We identified novel domains in the N- and C-terminal regions of the protein that are essential for localization, transposon repression, posterior patterning, and pole cell specification. One such functional region, the most C-terminal seven amino acids, is specific to Vas orthologues and is thus critical to distinguishing Vas from other closely related DEAD-box helicases. Surprisingly, we also found that many eGFP-Vas proteins carrying mutations that would be expected to abrogate DEAD-box helicase function localized to the nuage and posterior pole, and retained the capacity to support oogenesis, although they did not function in embryonic patterning, pole cell specification, grk activation, or transposon repression. We conclude from these experiments that Vas, a multifunctional protein, uses different domains and different molecular associations to carry out its various cellular and developmental roles.

  19. Functional interaction between Smad, CREB binding protein, and p68 RNA helicase

    International Nuclear Information System (INIS)

    Warner, Dennis R.; Bhattacherjee, Vasker; Yin, Xiaolong; Singh, Saurabh; Mukhopadhyay, Partha; Pisano, M. Michele; Greene, Robert M.

    2004-01-01

    The transforming growth factors β control a diversity of biological processes including cellular proliferation, differentiation, apoptosis, and extracellular matrix production, and are critical effectors of embryonic patterning and development, including that of the orofacial region. TGFβ superfamily members signal through specific cell surface receptors that phosphorylate the cytoplasmic Smad proteins, resulting in their translocation to the nucleus and interaction with promoters of TGFβ-responsive genes. Subsequent alterations in transcription are cell type-specific and dependent on recruitment to the Smad/transcription factor complex of coactivators, such as CBP and p300, or corepressors, such as c-ski and SnoN. Since the affinity of Smads for DNA is generally low, additional accessory proteins that facilitate Smad/DNA binding are required, and are often cell- and tissue-specific. In order to identify novel Smad 3 binding proteins in developing orofacial tissue, a yeast two hybrid assay was employed in which the MH2 domain of Smad 3 was used to screen an expression library derived from mouse embryonic orofacial tissue. The RNA helicase, p68, was identified as a unique Smad binding protein, and the specificity of the interaction was confirmed through various in vitro and in vivo assays. Co-expression of Smad 3 and a CBP-Gal4 DNA binding domain fusion protein in a Gal4-luciferase reporter assay resulted in increased TGFβ-stimulated reporter gene transcription. Moreover, co-expression of p68 RNA helicase along with Smad 3 and CBP-Gal4 resulted in synergistic activation of Gal4-luciferase reporter expression. Collectively, these data indicate that the RNA helicase, p68, can directly interact with Smad 3 resulting in formation of a transcriptionally active ternary complex containing Smad 3, p68, and CBP. This offers a means of enhancing TGFβ-mediated cellular responses in developing orofacial tissue

  20. Effects of additive application upon ad libitum intake, in vivo digestibility and nitrogen balance of alfalfa haylage

    Directory of Open Access Journals (Sweden)

    Mladen Knežević

    2009-09-01

    Full Text Available The research objective was to determine the effect of the additive Sill-All application on ad libitum intake, in vivo digestibility and nitrogen balance of alfalfa haylage. About 40 % alfalfa plants was ensiled at the phonological flowering stage into plastic foil-wrapped bales without or with additive (2 L t-1 plant mass. No statistically significant differences were found between alfalfa ensiled without additive and alfalfa ensiled with additive for the content of dry matter (DM (632 g and 631 g DM kg-1 fresh sample, respectively. Alfalfa ensiled without additive contained 921 g organic matter (OM kg-1 DM, which was significantly higher (P<0.001 compared to alfalfa ensiled with additive (902 g OM kg-1 DM. Alfalfa ensiled without additive contained 141 g crude proteins (CP kg-1 DM, which was significantly higher (P<0.001 compared to alfalfa ensiled with additive (139 g CP kg-1 DM. Alfalfa ensiled with additive contained significantly less acid detergent fibers (ADF (P<0.001 compared to alfalfa ensiled without additive (445 g kg-1 DM and 456 g kg-1 DM, respectively and had a lower pH value (P<0.001 (5.29 and 5.56, respectively. No statistically significant differences were found between the studied feeding treatments for ad libitum intake of fresh ration and DM ration, for the measured parameters of digestibility and N balance. It was concluded that addition of the additive to alfalfa haylage led to significant changes in chemical composition; however, changes in chemical composition had no impact on measured biological parameters (ad libitum intake, in vivo digestibility and nitrogen balance.

  1. Dissection of the functional domains of an archaeal holliday junction helicase

    DEFF Research Database (Denmark)

    Hong, Ye; Chu, Mingzhu; Li, Yansheng

    2012-01-01

    Helicases and nucleases form complexes that play very important roles in DNA repair pathways some of which interact with each other at Holliday junctions. In this study, we present in vitro and in vivo analysis of Hjm and its interaction with Hjc in Sulfolobus. In vitro studies employed Hjm from...... conformation change of the enzyme. Furthermore, StoHjm is able to prevent the formation of Hjc/HJ high complex, suggesting a regulation mechanism of Hjm to the activity of Hjc. We show that Hjm is essential for cell viability using recently developed genetic system and mutant propagation assay, suggesting...

  2. Yeast as a model system to study RecQ helicase function

    DEFF Research Database (Denmark)

    Ashton, Thomas M; Hickson, Ian David

    2010-01-01

    Mutations in the highly conserved RecQ helicase, BLM, cause the rare cancer predisposition disorder, Bloom's syndrome. The orthologues of BLM in Saccharomyces cerevisiae and Schizosaccharomyces pombe are SGS1 and rqh1(+), respectively. Studies in these yeast species have revealed a plethora...... of roles for the Sgs1 and Rqh1 proteins in repair of double strand breaks, restart of stalled replication forks, processing of aberrant intermediates that arise during meiotic recombination, and maintenance of telomeres. In this review, we focus on the known roles of Sgs1 and Rqh1 and how studies in yeast...

  3. New roles of the human Suv3 helicase in genome maintenance

    DEFF Research Database (Denmark)

    Venø, Susanne Trillingsgaard

    During her PhD studies, Susanne Trillingsgaard Venø carried out research into the role of the human Suv3 protein in stabilising the human genome – DNA. Suv3 is a helicase that separates the two strands of the DNA’s double helix. Throughout our lives, the DNA in our cells is constantly exposed...... maintenance. Based on these new research results, the Suv3 protein could be a valuable model for genome stability as an important factor in our understanding of why we get old....

  4. RTEL1: an essential helicase for telomere maintenance and the regulation of homologous recombination.

    Science.gov (United States)

    Uringa, Evert-Jan; Youds, Jillian L; Lisaingo, Kathleen; Lansdorp, Peter M; Boulton, Simon J

    2011-03-01

    Telomere maintenance and DNA repair are crucial processes that protect the genome against instability. RTEL1, an essential iron-sulfur cluster-containing helicase, is a dominant factor that controls telomere length in mice and is required for telomere integrity. In addition, RTEL1 promotes synthesis-dependent strand annealing to direct DNA double-strand breaks into non-crossover outcomes during mitotic repair and in meiosis. Here, we review the role of RTEL1 in telomere maintenance and homologous recombination and discuss models linking RTEL1's enzymatic activity to its function in telomere maintenance and DNA repair.

  5. Relationship of red and photographic infrared spectral radiances to alfalfa biomass, forage water content, percentage canopy cover, and severity of drought stress

    Science.gov (United States)

    Tucker, C. J.; Elgin, J. H., Jr.; Mcmurtrey, J. E., III

    1979-01-01

    Red and photographic infrared spectral data were collected using a handheld radiometer for two cuttings of alfalfa. Significant linear and non-linear correlation coefficients were found between the spectral variables and plant height, biomass, forage water content, and estimated canopy cover for the earlier alfalfa cutting. The alfalfa of later cutting experienced a period of severe drought stress which limited growth. The spectral variables were found to be highly correlated with the estimated drought scores for this alfalfa cutting.

  6. The helicase and ATPase activities of RECQL4 are compromised by mutations reported in three human patients

    DEFF Research Database (Denmark)

    Jensen, Martin Borch; Dunn, Christopher A; Keijzers, Guido

    2012-01-01

    RECQL4 is one of five members of the human RecQ helicase family, and is implicated in three syndromes displaying accelerating aging, developmental abnormalities and a predisposition to cancer. In this study, we purified three variants of RECQL4 carrying previously reported patient mutations....... These three mutant proteins were analyzed for the known biochemical activities of RECQL4: DNA binding, unwinding of duplex DNA, ATP hydrolysis and annealing of simplex DNA. Further, the mutant proteins were evaluated for stability and recruitment to sites of laser-induced DNA damage. One mutant was helicase...

  7. Identification of loci Associated with Resistance to Root-Rot Diseases in Autotetraploid Alfalfa using Genome-Wide Sequencing and Association Mapping

    Science.gov (United States)

    Alfalfa (Medicago sativa L.) is the world-wide forage crop. Changing trends to multipurpose uses increases demand for alfalfa. However, the production of alfalfa is challenged by endemic and emerging diseases. Identification of genes/loci controlling disease resistance will facilitate breeding for i...

  8. Occurrence of alfalfa (Medicago sativa L.) populations along roadsides in southern Manitoba, Canada and their potential role in intraspecific gene flow.

    Science.gov (United States)

    Bagavathiannan, Muthukumar V; Gulden, Robert H; Van Acker, Rene C

    2011-04-01

    Alfalfa is a highly outcrossing perennial species that can be noticed in roadsides as feral populations. There remains little information available on the extent of feral alfalfa populations in western Canadian prairies and their role in gene flow. The main objectives of this study were (a) to document the occurrence of feral alfalfa populations, and (b) to estimate the levels of outcrossing facilitated by feral populations. A roadside survey confirmed widespread occurrence of feral alfalfa populations, particularly in alfalfa growing regions. The feral populations were dynamic and their frequency ranged from 0.2 to 1.7 populations km(-1). In many cases, the nearest feral alfalfa population from alfalfa production field was located within a distance sufficient for outcrossing in alfalfa. The gene flow study confirmed that genes can move back and forth between feral and cultivated alfalfa populations. In this study, the estimated outcrossing levels were 62% (seed fields to feral), 78% (feral to seed fields), 82% (hay fields to feral) and 85% (feral to feral). Overall, the results show that feral alfalfa plants are prevalent in alfalfa producing regions in western Canada and they can serve as bridges for gene flow at landscape level. Management of feral populations should be considered, if gene flow is a concern. Emphasis on preventing seed spill/escapes and intentional roadside planting of alfalfa cultivars will be particularly helpful. Further, realistic and pragmatic threshold levels should be established for markets sensitive to the presence of GE traits.

  9. 7 CFR 202.44 - Proceedings under section 305(b) to determine whether foreign alfalfa or red clover seed is not...

    Science.gov (United States)

    2010-01-01

    ... foreign alfalfa or red clover seed is not adapted for general agricultural use in the United States. 202... Proceedings under section 305(b) to determine whether foreign alfalfa or red clover seed is not adapted for... for the purpose of determining whether seed of alfalfa or red clover from any foreign country or...

  10. Transgene silencing of sucrose synthase in alfalfa (Medicago sativa L.) stem vascular tissue suggests a role for invertase in cell wall cellulose synthesis

    Science.gov (United States)

    Alfalfa (Medicago sativa L.) plants were transformed with two constructs: (1) a truncated phosphoenolpyruvate carboxylase promoter isolated from alfalfa nodules (PEPC-4) fused to GUS; and (2) PEPC-4 fused with sucrose synthase (SUS) isolated from alfalfa nodules. Histochemical staining for GUS in st...

  11. Yield, yield components and dry matter digestibility of alfalfa experimental populations

    Directory of Open Access Journals (Sweden)

    Katić Slobodan

    2010-01-01

    Full Text Available Alfalfa is the most important forage crop grown in the temperate regions. It is cultivated for production of vegetative aerial mass used fresh or as hay, and recently as haylage and silage. In many centres worldwide, efforts are made to breed and create new alfalfa cultivars with both higher yields and of higher nutritional value. The aim of this paper was to determine yield and digestibility of 12 experimental populations of alfalfa, and to compare their results to the yields of well-known domestic alfalfa commercial cultivars. The results show significant differences in yield of green forage and dry matter among alfalfa populations, as well as in yield components, height, proportion of leaves in yield and growth rate (tab. 1, 2 and 3. Differences between in vitro digestible dry matter (% and yields of in vitro digestible dry matter (t ha-1 were also significant (tab. 5 and 6. Yield and quality of experimental populations were at the same level or higher than of control cultivars. Synthetic SINUSA exceeded the control cutivars (NS Mediana ZMS V and Banat VS in yield and quality of dry matter. .

  12. Alfalfa dodder (Cuscuta campestris) toxicity in horses: clinical, haematological and serum biochemical findings.

    Science.gov (United States)

    Abutarbush, S M

    2013-07-27

    The objective of this observational study is to describe clinical, haematological and serum biochemical findings of horses affected with alfalfa dodder (Cuscuta campestris) toxicity. Twenty horses naturally exposed to alfalfa dodder toxicity were examined and information was collected on history and clinical signs. Physical examination was done on horses in the premises (n=20), and venous blood samples of 12 horses were submitted for haematology and serum biochemical examination for each horse. Abnormal clinical signs started around 36 hours after horses were fed the contaminated alfalfa. Abnormal signs were seen in 11 horses and those included diarrhoea (n=8), decreased appetite (n=7), neurological signs (n=4) and abdominal pain (n=1). Some horses had multiple clinical signs of the above. The results of complete blood cell count revealed leukocytopenia, neutropenia and thrombocytopenia. Serum biochemical analysis revealed decreased ALP, AST and CPK levels and increased direct bilirubin level. The used alfalfa was stopped immediately and a different alfalfa from a new container that did not contain any weeds was fed. Horses on the premises were observed closely, and the abnormal clinical signs resolved within three days. No treatment was implemented. Knowledge about toxicity of horses by Cuscuta species is scarce in the English veterinary literature and very limited.

  13. The Role of Proanthocyanidins Complex in Structure and Nutrition Interaction in Alfalfa Forage

    Directory of Open Access Journals (Sweden)

    Arjan Jonker

    2016-05-01

    Full Text Available Alfalfa (Medicago sativa L. is one of the main forages grown in the world. Alfalfa is a winter hardy, drought tolerant, N-fixing legume with a good longevity, high yield, high nutrient levels, high digestibility, unique structural to non-structural components ratio, high dry matter intake, and high animal productivity per hectare. However, its main limitation is its excessively rapid initial rate of protein degradation in the rumen, which results in pasture bloat and inefficient use of protein with consequent excessive excretions of nitrogen into the environment. Proanthocyanidins are secondary plant metabolites that can bind with protein and thereby reduce the rate and extent of ruminal protein degradation. However, these secondary metabolites do not accumulate in alfalfa. This review aims to firstly describe the events involved in the rapid release of protein from alfalfa and its effect on ruminant nutrition, environmental pollution, and pasture bloat; secondly, to describe occurrence, structure, functions and benefits of moderate amounts of proanthocyanidin; and finally, to describe the development of alfalfa which accumulates moderate amounts of proanthocyanidins. The emphasis of this review focuses on the role of proanthocyanidins compounds in structure and nutrition interaction in ruminant livestock systems.

  14. The Role of Proanthocyanidins Complex in Structure and Nutrition Interaction in Alfalfa Forage.

    Science.gov (United States)

    Jonker, Arjan; Yu, Peiqiang

    2016-05-23

    Alfalfa (Medicago sativa L.) is one of the main forages grown in the world. Alfalfa is a winter hardy, drought tolerant, N-fixing legume with a good longevity, high yield, high nutrient levels, high digestibility, unique structural to non-structural components ratio, high dry matter intake, and high animal productivity per hectare. However, its main limitation is its excessively rapid initial rate of protein degradation in the rumen, which results in pasture bloat and inefficient use of protein with consequent excessive excretions of nitrogen into the environment. Proanthocyanidins are secondary plant metabolites that can bind with protein and thereby reduce the rate and extent of ruminal protein degradation. However, these secondary metabolites do not accumulate in alfalfa. This review aims to firstly describe the events involved in the rapid release of protein from alfalfa and its effect on ruminant nutrition, environmental pollution, and pasture bloat; secondly, to describe occurrence, structure, functions and benefits of moderate amounts of proanthocyanidin; and finally, to describe the development of alfalfa which accumulates moderate amounts of proanthocyanidins. The emphasis of this review focuses on the role of proanthocyanidins compounds in structure and nutrition interaction in ruminant livestock systems.

  15. Accumulation and residue of napropamide in alfalfa (Medicago sativa) and soil involved in toxic response.

    Science.gov (United States)

    Cui, Li E; Yang, Hong

    2011-06-15

    Napropamide belongs to the amide herbicide family and widely used to control weeds in farmland. Intensive use of the herbicide has resulted in widespread contamination to ecosystems. The present study demonstrated an analysis on accumulation of the toxic pesticide napropamide in six genotypes of alfalfa (Medicago sativa), along with biological parameters and its residues in soils. Soil was treated with napropamide at 3 mg kg(-1) dry soil and alfalfa plants were cultured for 10 or 30 d, respectively. The maximum value for napropamide accumulation is 0.426 mg kg(-1) in shoots and 2.444 mg kg(-1) in roots. The napropamide-contaminated soil with alfalfa cultivation had much lower napropamide concentrations than the control (soil without alfalfa cultivation). Also, the content of napropamide residue in the rhizosphere was significantly lower than that in the non-rhizosphere soil. M. sativa exposed to 3 mg kg(-1) napropamide showed inhibited growth. Further analysis revealed that plants treated with napropamide accumulated more reactive oxygen species (O(2)(-) and H(2)O(2)) and less amounts of chlorophyll. However, not all cultivars showed oxidative injury, suggesting that the alfalfa cultivars display different tolerance to napropamide. Copyright © 2011 Elsevier B.V. All rights reserved.

  16. Transgenic Alfalfa Plants Expressing the Sweetpotato Orange Gene Exhibit Enhanced Abiotic Stress Tolerance

    Science.gov (United States)

    Wang, Zhi; Ke, Qingbo; Kim, Myoung Duck; Kim, Sun Ha; Ji, Chang Yoon; Jeong, Jae Cheol; Lee, Haeng-Soon; Park, Woo Sung; Ahn, Mi-Jeong; Li, Hongbing; Xu, Bingcheng; Deng, Xiping; Lee, Sang-Hoon; Lim, Yong Pyo; Kwak, Sang-Soo

    2015-01-01

    Alfalfa (Medicago sativa L.), a perennial forage crop with high nutritional content, is widely distributed in various environments worldwide. We recently demonstrated that the sweetpotato Orange gene (IbOr) is involved in increasing carotenoid accumulation and enhancing resistance to multiple abiotic stresses. In this study, in an effort to improve the nutritional quality and environmental stress tolerance of alfalfa, we transferred the IbOr gene into alfalfa (cv. Xinjiang Daye) under the control of an oxidative stress-inducible peroxidase (SWPA2) promoter through Agrobacterium tumefaciens-mediated transformation. Among the 11 transgenic alfalfa lines (referred to as SOR plants), three lines (SOR2, SOR3, and SOR8) selected based on their IbOr transcript levels were examined for their tolerance to methyl viologen (MV)-induced oxidative stress in a leaf disc assay. The SOR plants exhibited less damage in response to MV-mediated oxidative stress and salt stress than non-transgenic plants. The SOR plants also exhibited enhanced tolerance to drought stress, along with higher total carotenoid levels. The results suggest that SOR alfalfa plants would be useful as forage crops with improved nutritional value and increased tolerance to multiple abiotic stresses, which would enhance the development of sustainable agriculture on marginal lands. PMID:25946429

  17. A comparison of ground beetle assemblages (Coleoptera: Carabidae in conventionally and ecologically managed alfalfa fields

    Directory of Open Access Journals (Sweden)

    P. Kolařík

    2014-12-01

    Full Text Available From 2007-2011, the occurrence of ground beetles (Coleoptera: Carabidae was studied using emergence traps in two differently managed alfalfa fields in the Czech Republic - a conventional and an ecological production system. In total, 784 specimens of ground beetles representing 58 species were trapped in these two alfalfa fields in South Moravia. A slightly higher number of specimens were trapped in the conventionally managed than in the ecological alfalfa stand (404 vs 380, respectively. In the conventionally managed alfalfa stand, the number of species was also higher than in the ecological stand (45 vs 40, respectively. With the exception of 2007 and 2009, Simpson’s indices of diversity were higher in the conventional stand than in the ecological in all study years. Shannon’s index was higher in the conventional alfalfa field in 2008, 2009, and 2011. Regarding distribution, species classified into group E (i.e., those without special demands on the type and quality of their habitat dominated in both types of management throughout the experimental period. The incidence of species classified into group R (i.e., those with narrow ecological amplitude was very low; i.e., only four species. These ground beetle species are included in the Red List of Threatened Species of the Czech Republic, and all of them (i.e. Acupalpus suturalis, Calosoma auropunctatum, Cicindela germanica and Ophonus cribricollis are listed as vulnerable.

  18. Single-Feature Polymorphism Discovery in the Transcriptome of Tetraploid Alfalfa

    Directory of Open Access Journals (Sweden)

    S. Samuel Yang

    2009-11-01

    Full Text Available Advances in alfalfa [ (L. subsp. ] breeding, molecular genetics, and genomics have been slow because this crop is an allogamous autotetraploid (2n = 4x = 32 with complex polysomic inheritance and few genomic resources. Increasing cellulose and decreasing lignin in alfalfa stem cell walls would improve this crop as a cellulosic ethanol feedstock. We conducted genome-wide analysis of single-feature polymorphisms (SFPs of two alfalfa genotypes (252, 1283 that differ in stem cell wall lignin and cellulose concentrations. SFP analysis was conducted using the GeneChip (Affymetrix, Santa Clara, CA as a cross-species platform. Analysis of GeneChip expression data files of alfalfa stem internodes of genotypes 252 and 1283 at two growth stages (elongating, post-elongation revealed 10,890 SFPs in 8230 probe sets. Validation analysis by polymerase chain reaction (PCR-sequencing of a random sample of SFPs indicated a 17% false discovery rate. Functional classification and over-representation analysis showed that genes involved in photosynthesis, stress response and cell wall biosynthesis were highly enriched among SFP-harboring genes. The GeneChip is a suitable cross-species platform for detecting SFPs in tetraploid alfalfa.

  19. The ALFALFA Extragalactic Catalog and Data Processing Pipeline

    Science.gov (United States)

    Kent, Brian R.; Haynes, Martha P.; Giovanelli, Riccardo; ALFALFA Team

    2018-06-01

    The Arecibo Legacy Fast ALFA 21cm HI Survey has reached completion. The observations and data are used by team members and the astronomical community in a variety of scientific initiatives with gas-rich galaxies, cluster environments, and studies of low redshift cosmology. The survey covers nearly 7000 square degrees of high galactic latitude sky visible from Arecibo, Puerto Rico and ~4400 hours of observations from 2005 to 2011. We present the extragalactic HI source catalog of over ~31,000 detections, their measured properties, and associated derived parameters. The observations were carefully reduced using a custom made data reduction pipeline and interface. Team members interacted with this pipeline through observation planning, calibration, imaging, source extraction, and cataloging. We describe this processing workflow as it pertains to the complexities of the single-dish multi-feed data reduction as well as known caveats of the source catalog and spectra for use in future astronomical studies and analysis. The ALFALFA team at Cornell has been supported by NSF grants AST-0607007, AST-1107390 and AST-1714828 and by grants from the Brinson Foundation.

  20. Deriving Stellar Masses for the ALFALFA α.100 Sample

    Science.gov (United States)

    Hess, Logan; Cornell 2017 Summer REU

    2018-01-01

    For this project, we explore different methods of deriving the stellar masses of galaxies in the ALFALFA (Arecibo Legacy Fast ALFA) α.100 survey. In particular, we measure the effectiveness of SED (Spectral Energy Distribution) on the sample. SED fitting was preformed by MAGPHYS (Multi-wavelength Analysis of Galaxy Physical Properties), utilizing a wide range of photometry in the UV, optical, and IR bands. Photometry was taken from GALAX GR6/7 (UV), SDSS DR13 (optical), WISE All-Sky (near-IR), and Herschel PACS/SPIRE (far-IR). The efficiency of SED fitting increases with a broader range of photometry, however detection rates varied significantly across the different bands. Using a more “comprehensive” sample of galaxies, the GSWLC-A (GALAX, SDSS, WISE Legacy Catalog All-Sky Survey), we aimed to measure which combination of bands provided the largest sample return with the lowest amount of uncertainty, which could then be used to estimate the masses of the galaxies in the α.100 sample.

  1. Effect of aflatoxin B1 on in vitro ruminal fermentation of rations high in alfalfa hay or ryegrass hay

    DEFF Research Database (Denmark)

    Jiang, Y H; Yang, H J; Lund, Peter

    2012-01-01

    A 2 × 4 factorial experiment was conducted to determine the effect of aflatoxin B1 (AFB1) at dose rates of 0, 320, 640, 960 ng/ml on ruminal fermentation of substrates high in alfalfa hay (HA, alfalfa hay: maize meal = 4:1) and ryegrass hay (HR, ryegrass hay: maize meal = 4:1). In vitro dry matter...

  2. Variation in alfalfa leafcutting bee (hymenoptera: megachilidae) reproductive success according to location of nests in United States commercial domiciles.

    Science.gov (United States)

    Low, medium, and high stocking densities of Megachile rotundata, the alfalfa leafcutting bee, were released over four years in three research plots of Utah alfalfa planted at seed-production rates. A low number of bees (46-79% of released) survived the incubation and field emergence processes, and ...

  3. Effects of supplementation level and particle size of alfalfa hay on growth characteristics and rumen development in dairy calves

    NARCIS (Netherlands)

    Mirzaei, M.; Khorvash, M.; Ghorbani, G.R.; Kazemi-Bonchenari, M.; Riasi, A.; Nabipour, A.; Borne, van den J.J.G.C.

    2015-01-01

    The aim of this study was to assess the effects of particle size (PS) of alfalfa hay on growth characteristics and rumen development in dairy calves at two levels of alfalfa supplementation. Fifty newborn dairy calves (42.7 ± 2.2 kg BW) were used in a 2 × 2 factorial arrangement with the factors

  4. Dna2 nuclease-helicase structure, mechanism and regulation by Rpa.

    Science.gov (United States)

    Zhou, Chun; Pourmal, Sergei; Pavletich, Nikola P

    2015-11-02

    The Dna2 nuclease-helicase maintains genomic integrity by processing DNA double-strand breaks, Okazaki fragments and stalled replication forks. Dna2 requires ssDNA ends, and is dependent on the ssDNA-binding protein Rpa, which controls cleavage polarity. Here we present the 2.3 Å structure of intact mouse Dna2 bound to a 15-nucleotide ssDNA. The nuclease active site is embedded in a long, narrow tunnel through which the DNA has to thread. The helicase domain is required for DNA binding but not threading. We also present the structure of a flexibly-tethered Dna2-Rpa interaction that recruits Dna2 to Rpa-coated DNA. We establish that a second Dna2-Rpa interaction is mutually exclusive with Rpa-DNA interactions and mediates the displacement of Rpa from ssDNA. This interaction occurs at the nuclease tunnel entrance and the 5' end of the Rpa-DNA complex. Hence, it only displaces Rpa from the 5' but not 3' end, explaining how Rpa regulates cleavage polarity.

  5. The nuclear import of RNA helicase A is mediated by importin-α3

    International Nuclear Information System (INIS)

    Aratani, Satoko; Oishi, Takayuki; Fujita, Hidetoshi; Nakazawa, Minako; Fujii, Ryouji; Imamoto, Naoko; Yoneda, Yoshihiro; Fukamizu, Akiyoshi; Nakajima, Toshihiro

    2006-01-01

    RNA helicase A (RHA), an ATPase/helicase, regulates the gene expression at various steps including transcriptional activation and RNA processing. RHA is known to shuttle between the nucleus and cytoplasm. We identified the nuclear localization signal (NLS) of RHA and analyzed the nuclear import mechanisms. The NLS of RHA (RHA-NLS) consisting of 19 amino acid residues is highly conserved through species and does not have the consensus classical NLS. In vitro nuclear import assays revealed that the nuclear import of RHA was Ran-dependent and mediated with the classical importin-α/β-dependent pathway. The binding assay indicated that the basic residues in RHA-NLS were used for interaction with importin-α. Furthermore, the nuclear import of RHA-NLS was supported by importin-α1 and preferentially importin-α3. Our results indicate that the nuclear import of RHA is mediated by the importin-α3/importin-β-dependent pathway and suggest that the specificity for importin may regulate the functions of cargo proteins

  6. Bloom syndrome helicase in meiosis: Pro-crossover functions of an anti-crossover protein.

    Science.gov (United States)

    Hatkevich, Talia; Sekelsky, Jeff

    2017-09-01

    The functions of the Bloom syndrome helicase (BLM) and its orthologs are well characterized in mitotic DNA damage repair, but their roles within the context of meiotic recombination are less clear. In meiotic recombination, multiple repair pathways are used to repair meiotic DSBs, and current studies suggest that BLM may regulate the use of these pathways. Based on literature from Saccharomyces cerevisiae, Arabidopsis thaliana, Mus musculus, Drosophila melanogaster, and Caenorhabditis elegans, we present a unified model for a critical meiotic role of BLM and its orthologs. In this model, BLM and its orthologs utilize helicase activity to regulate the use of various pathways in meiotic recombination by continuously disassembling recombination intermediates. This unwinding activity provides the meiotic program with a steady pool of early recombination substrates, increasing the probability for a DSB to be processed by the appropriate pathway. As a result of BLM activity, crossovers are properly placed throughout the genome, promoting proper chromosomal disjunction at the end of meiosis. This unified model can be used to further refine the complex role of BLM and its orthologs in meiotic recombination. © 2017 WILEY Periodicals, Inc.

  7. Real-time electrochemical monitoring of isothermal helicase-dependent amplification of nucleic acids.

    Science.gov (United States)

    Kivlehan, Francine; Mavré, François; Talini, Luc; Limoges, Benoît; Marchal, Damien

    2011-09-21

    We described an electrochemical method to monitor in real-time the isothermal helicase-dependent amplification of nucleic acids. The principle of detection is simple and well-adapted to the development of portable, easy-to-use and inexpensive nucleic acids detection technologies. It consists of monitoring a decrease in the electrochemical current response of a reporter DNA intercalating redox probe during the isothermal DNA amplification. The method offers the possibility to quantitatively analyze target nucleic acids in less than one hour at a single constant temperature, and to perform at the end of the isothermal amplification a DNA melt curve analysis for differentiating between specific and non-specific amplifications. To illustrate the potentialities of this approach for the development of a simple, robust and low-cost instrument with high throughput capability, the method was validated with an electrochemical system capable of monitoring up to 48 real-time isothermal HDA reactions simultaneously in a disposable microplate consisting of 48-electrochemical microwells. Results obtained with this approach are comparable to that obtained with a well-established but more sophisticated and expensive fluorescence-based method. This makes for a promising alternative detection method not only for real-time isothermal helicase-dependent amplification of nucleic acid, but also for other isothermal DNA amplification strategies.

  8. Mcm10 regulates DNA replication elongation by stimulating the CMG replicative helicase.

    Science.gov (United States)

    Lõoke, Marko; Maloney, Michael F; Bell, Stephen P

    2017-02-01

    Activation of the Mcm2-7 replicative DNA helicase is the committed step in eukaryotic DNA replication initiation. Although Mcm2-7 activation requires binding of the helicase-activating proteins Cdc45 and GINS (forming the CMG complex), an additional protein, Mcm10, drives initial origin DNA unwinding by an unknown mechanism. We show that Mcm10 binds a conserved motif located between the oligonucleotide/oligosaccharide fold (OB-fold) and A subdomain of Mcm2. Although buried in the interface between these domains in Mcm2-7 structures, mutations predicted to separate the domains and expose this motif restore growth to conditional-lethal MCM10 mutant cells. We found that, in addition to stimulating initial DNA unwinding, Mcm10 stabilizes Cdc45 and GINS association with Mcm2-7 and stimulates replication elongation in vivo and in vitro. Furthermore, we identified a lethal allele of MCM10 that stimulates initial DNA unwinding but is defective in replication elongation and CMG binding. Our findings expand the roles of Mcm10 during DNA replication and suggest a new model for Mcm10 function as an activator of the CMG complex throughout DNA replication. © 2017 Lõoke et al.; Published by Cold Spring Harbor Laboratory Press.

  9. G-quadruplexes Significantly Stimulate Pif1 Helicase-catalyzed Duplex DNA Unwinding*

    Science.gov (United States)

    Duan, Xiao-Lei; Liu, Na-Nv; Yang, Yan-Tao; Li, Hai-Hong; Li, Ming; Dou, Shuo-Xing; Xi, Xu-Guang

    2015-01-01

    The evolutionarily conserved G-quadruplexes (G4s) are faithfully inherited and serve a variety of cellular functions such as telomere maintenance, gene regulation, DNA replication initiation, and epigenetic regulation. Different from the Watson-Crick base-pairing found in duplex DNA, G4s are formed via Hoogsteen base pairing and are very stable and compact DNA structures. Failure of untangling them in the cell impedes DNA-based transactions and leads to genome instability. Cells have evolved highly specific helicases to resolve G4 structures. We used a recombinant nuclear form of Saccharomyces cerevisiae Pif1 to characterize Pif1-mediated DNA unwinding with a substrate mimicking an ongoing lagging strand synthesis stalled by G4s, which resembles a replication origin and a G4-structured flap in Okazaki fragment maturation. We find that the presence of G4 may greatly stimulate the Pif1 helicase to unwind duplex DNA. Further studies reveal that this stimulation results from G4-enhanced Pif1 dimerization, which is required for duplex DNA unwinding. This finding provides new insights into the properties and functions of G4s. We discuss the observed activation phenomenon in relation to the possible regulatory role of G4s in the rapid rescue of the stalled lagging strand synthesis by helping the replicator recognize and activate the replication origin as well as by quickly removing the G4-structured flap during Okazaki fragment maturation. PMID:25627683

  10. Germline mutations of regulator of telomere elongation helicase 1, RTEL1, in Dyskeratosis congenita.

    Science.gov (United States)

    Ballew, Bari J; Yeager, Meredith; Jacobs, Kevin; Giri, Neelam; Boland, Joseph; Burdett, Laurie; Alter, Blanche P; Savage, Sharon A

    2013-04-01

    Dyskeratosis congenita (DC) is an inherited bone marrow failure and cancer predisposition syndrome caused by aberrant telomere biology. The classic triad of dysplastic nails, abnormal skin pigmentation, and oral leukoplakia is diagnostic of DC, but substantial clinical heterogeneity exists; the clinically severe variant Hoyeraal Hreidarsson syndrome (HH) also includes cerebellar hypoplasia, severe immunodeficiency, enteropathy, and intrauterine growth retardation. Germline mutations in telomere biology genes account for approximately one-half of known DC families. Using exome sequencing, we identified mutations in RTEL1, a helicase with critical telomeric functions, in two families with HH. In the first family, two siblings with HH and very short telomeres inherited a premature stop codon from their mother who has short telomeres. The proband from the second family has HH and inherited a premature stop codon in RTEL1 from his father and a missense mutation from his mother, who also has short telomeres. In addition, inheritance of only the missense mutation led to very short telomeres in the proband's brother. Targeted sequencing identified a different RTEL1 missense mutation in one additional DC proband who has bone marrow failure and short telomeres. Both missense mutations affect the helicase domain of RTEL1, and three in silico prediction algorithms suggest that they are likely deleterious. The nonsense mutations both cause truncation of the RTEL1 protein, resulting in loss of the PIP box; this may abrogate an important protein-protein interaction. These findings implicate a new telomere biology gene, RTEL1, in the etiology of DC.

  11. Characterization of the Caenorhabditis elegans HIM-6/BLM helicase: unwinding recombination intermediates.

    Science.gov (United States)

    Jung, Hana; Lee, Jin A; Choi, Seoyoon; Lee, Hyunwoo; Ahn, Byungchan

    2014-01-01

    Mutations in three human RecQ genes are implicated in heritable human syndromes. Mutations in BLM, a RecQ gene, cause Bloom syndrome (BS), which is characterized by short stature, cancer predisposition, and sensitivity to sunlight. BLM is a RecQ DNA helicase that, with interacting proteins, is able to dissolve various DNA structures including double Holliday junctions. A BLM ortholog, him-6, has been identified in Caenorhabditis elegans, but little is known about its enzymatic activities or its in vivo roles. By purifying recombinant HIM-6 and performing biochemical assays, we determined that the HIM-6 has DNA-dependent ATPase activity HIM-6 and helicase activity that proceeds in the 3'-5' direction and needs at least five 3' overhanging nucleotides. HIM-6 is also able to unwind DNA structures including D-loops and Holliday junctions. Worms with him-6 mutations were defective in recovering the cell cycle arrest after HU treatment. These activities strongly support in vivo roles for HIM-6 in processing recombination intermediates.

  12. Requirement for the E1 Helicase C-Terminal Domain in Papillomavirus DNA Replication In Vivo.

    Science.gov (United States)

    Bergvall, Monika; Gagnon, David; Titolo, Steve; Lehoux, Michaël; D'Abramo, Claudia M; Melendy, Thomas; Archambault, Jacques

    2016-01-06

    The papillomavirus (PV) E1 helicase contains a conserved C-terminal domain (CTD), located next to its ATP-binding site, whose function in vivo is still poorly understood. The CTD is comprised of an alpha helix followed by an acidic region (AR) and a C-terminal extension termed the C-tail. Recent biochemical studies on bovine papillomavirus 1 (BPV1) E1 showed that the AR and C-tail regulate the oligomerization of the protein into a double hexamer at the origin. In this study, we assessed the importance of the CTD of human papillomavirus 11 (HPV11) E1 in vivo, using a cell-based DNA replication assay. Our results indicate that combined deletion of the AR and C-tail drastically reduces DNA replication, by 85%, and that further truncation into the alpha-helical region compromises the structural integrity of the E1 helicase domain and its interaction with E2. Surprisingly, removal of the C-tail alone or mutation of highly conserved residues within the domain still allows significant levels of DNA replication (55%). This is in contrast to the absolute requirement for the C-tail reported for BPV1 E1 in vitro and confirmed here in vivo. Characterization of chimeric proteins in which the AR and C-tail from HPV11 E1 were replaced by those of BPV1 indicated that while the function of the AR is transferable, that of the C-tail is not. Collectively, these findings define the contribution of the three CTD subdomains to the DNA replication activity of E1 in vivo and suggest that the function of the C-tail has evolved in a PV type-specific manner. While much is known about hexameric DNA helicases from superfamily 3, the papillomavirus E1 helicase contains a unique C-terminal domain (CTD) adjacent to its ATP-binding site. We show here that this CTD is important for the DNA replication activity of HPV11 E1 in vivo and that it can be divided into three functional subdomains that roughly correspond to the three conserved regions of the CTD: an alpha helix, needed for the structural

  13. Requirement for the E1 Helicase C-Terminal Domain in Papillomavirus DNA Replication In Vivo

    Science.gov (United States)

    Bergvall, Monika; Gagnon, David; Titolo, Steve; Lehoux, Michaël; D'Abramo, Claudia M.

    2016-01-01

    ABSTRACT The papillomavirus (PV) E1 helicase contains a conserved C-terminal domain (CTD), located next to its ATP-binding site, whose function in vivo is still poorly understood. The CTD is comprised of an alpha helix followed by an acidic region (AR) and a C-terminal extension termed the C-tail. Recent biochemical studies on bovine papillomavirus 1 (BPV1) E1 showed that the AR and C-tail regulate the oligomerization of the protein into a double hexamer at the origin. In this study, we assessed the importance of the CTD of human papillomavirus 11 (HPV11) E1 in vivo, using a cell-based DNA replication assay. Our results indicate that combined deletion of the AR and C-tail drastically reduces DNA replication, by 85%, and that further truncation into the alpha-helical region compromises the structural integrity of the E1 helicase domain and its interaction with E2. Surprisingly, removal of the C-tail alone or mutation of highly conserved residues within the domain still allows significant levels of DNA replication (55%). This is in contrast to the absolute requirement for the C-tail reported for BPV1 E1 in vitro and confirmed here in vivo. Characterization of chimeric proteins in which the AR and C-tail from HPV11 E1 were replaced by those of BPV1 indicated that while the function of the AR is transferable, that of the C-tail is not. Collectively, these findings define the contribution of the three CTD subdomains to the DNA replication activity of E1 in vivo and suggest that the function of the C-tail has evolved in a PV type-specific manner. IMPORTANCE While much is known about hexameric DNA helicases from superfamily 3, the papillomavirus E1 helicase contains a unique C-terminal domain (CTD) adjacent to its ATP-binding site. We show here that this CTD is important for the DNA replication activity of HPV11 E1 in vivo and that it can be divided into three functional subdomains that roughly correspond to the three conserved regions of the CTD: an alpha helix, needed

  14. Water sensors with cellular system eliminate tail water drainage in alfalfa irrigation

    Directory of Open Access Journals (Sweden)

    Rajat Saha

    2011-10-01

    Full Text Available Alfalfa is the largest consumer of water among all crops in California. It is generally flood-irrigated, so any system that decreases runoff can improve irrigation efficiency and conserve water. To more accurately manage the water flow at the tail (bottom end of the field in surface-irrigated alfalfa crops, we developed a system that consists of wetting-front sensors, a cellular communication system and a water advance model. This system detects the wetting front, determines its advance rate and generates a cell-phone alert to the irrigator when the water supply needs to be cut off, so that tail water drainage is minimized. To test its feasibility, we conducted field tests during the 2008 and 2009 alfalfa growing seasons. The field experiments successfully validated the methodology, producing zero tail water drainage.

  15. Monolignol biosynthesis in microsomal preparations from lignifying stems of alfalfa (Medicago sativa L.).

    Science.gov (United States)

    Guo, Dianjing; Chen, Fang; Dixon, Richard A

    2002-11-01

    Microsomal preparations from lignifying stems of alfalfa (Medicago sativa L.) contained coniferaldehyde 5-hydroxylase activity and immunodetectable caffeic acid 3-O-methyltransferase (COMT), and catalyzed the S-adenosyl L-methionine (SAM) dependent methylation of caffeic acid, caffeyl aldehyde and caffeyl alcohol. When supplied with NADPH and SAM, the microsomes converted caffeyl aldehyde to coniferaldehyde, 5-hydroxyconiferaldehyde, and traces of sinapaldehyde. Coniferaldehyde was a better precursor of sinapaldehyde than was 5-hydroxyconiferaldehyde. The alfalfa microsomes could not metabolize 4-coumaric acid, 4-coumaraldehyde, 4-coumaroyl CoA, or ferulic acid. No metabolism of monolignol precursors was observed in microsomal preparations from transgenic alfalfa down-regulated in COMT expression. In most microsomal preparations, the level of the metabolic conversions was independent of added recombinant COMT. Taken together, the data provide only limited support for the concept of metabolic channeling in the biosynthesis of S monolignols via coniferaldehyde.

  16. Yields of alfalfa varieties with different fall dormancy levels in northeast china

    International Nuclear Information System (INIS)

    Chen, J.S.; Zhu, R.F.; Di, G.L.

    2014-01-01

    Fall dormancy (FD) is an important indicator of winter hardiness in alfalfa (Medicago sativa L.), the relationship between FD and the yield potential of alfalfa varieties were investigated to survey annual dry matter (DM) yields with FD levels in the northeast regions with cold winters. During three consecutive years, all varieties of five FD levels survived over the winter without any persistency problems and there were no differences in annual DM yields of varieties among FD levels. Among the same FD varieties, DM yields for some of the dormant, semi-dormant and non-dormant varieties were found no correlated with FD levels. In conclusion, it suggests that different FD levels no effected on yields of alfalfa in the cold regions, such as North-east China. (author)

  17. Flavonoids released naturally from alfalfa promote development of symbiotic glomus spores in vitro.

    Science.gov (United States)

    Tsai, S M; Phillips, D A

    1991-05-01

    Because flavonoids from legumes induce transcription of nodulation genes in symbiotic rhizobial bacteria, it is reasonable to test whether these compounds alter the development of vesicular-arbuscular mycorrhizal (VAM) fungi that infect those plants. Quercetin-3-O-galactoside, the dominant flavonoid released naturally from alfalfa (Medicago sativa L.) seeds, promoted spore germination of Glomus etunicatum and Glomus macrocarpum in vitro. Quercetin produced the maximum increases in spore germination, hyphal elongation, and hyphal branching in G. etunicatum at 1 to 2.5 muM concentrations. Two flavonoids exuded from alfalfa roots, 4',7-dihydroxyflavone and 4',7-dihydroxyflavanone, also enhanced spore germination of this fungal species. Formononetin, an isoflavone that is released from stressed alfalfa roots, inhibited germination of both Glomus species. These in vitro results suggest that plant flavonoids may facilitate or regulate the development of VAM symbioses and offer new hope for developing pure, plant-free cultures of VAM fungi.

  18. Water savings from reduced alfalfa cropping in California's Upper San Joaquin Valley

    Science.gov (United States)

    Singh, K. K.; Gray, J.

    2017-12-01

    Water and food and forage security are inextricably linked. In fact, 90% of global freshwater is consumed for food production. Food demand increases as populations grow and diets change, making water increasingly scarce. This tension is particularly acute, contentious, and popularly appreciated in California's Central Valley, which is one of the most important non-grain cropping areas in the United States. While the water-intensive production of tree nuts like almonds and pistachios has received the most popular attention, it is California's nation-leading alfalfa production that consumes the most water. Alfalfa, the "Queen of Forages" is the preferred feedstock for California's prodigious dairy industry. It is grown year-round, and single fields can be harvested more than four times a year; a practice which can require in excess of 1.5 m of irrigation water. Given the water scarcity in the region, the production of alfalfa is under increasing scrutiny with respect to long-term sustainability. However, the potential water savings associated with alternative crops, and various levels of alfalfa replacement have not been quantified. Here, we address that knowledge gap by simulating the ecohydrology of the Upper San Joaquin's cropping system under various scenarios of alfalfa crop replacement with crops of comparable economic value. Specifically, we use the SWAT model to evaluate the water savings that would be realized at 33%, 66%, and 100% alfalfa replacement with economically comparable, but more water efficient crops such as tomatoes. Our results provide an important quantification of the potential water savings under alternative cropping systems that, importantly, also addresses the economic concerns of farmers. Results like these provide critical guidance to farmers and land/water decision makers as they plan for a more sustainable and productive agricultural future.

  19. Human SUV3 helicase regulates growth rate of the HeLa cells and can localize in the nucleoli.

    Science.gov (United States)

    Szewczyk, Maciej; Fedoryszak-Kuśka, Natalia; Tkaczuk, Katarzyna; Dobrucki, Jurek; Waligórska, Agnieszka; Stępień, Piotr P

    2017-01-01

    The human SUV3 helicase (SUV3, hSUV3, SUPV3L1) is a DNA/RNA unwinding enzyme belonging to the class of DexH-box helicases. It localizes predominantly in the mitochondria, where it forms an RNA-degrading complex called mitochondrial degradosome with exonuclease PNP (polynucleotide phosphorylase). Association of this complex with the polyA polymerase can modulate mitochondrial polyA tails. Silencing of the SUV3 gene was shown to inhibit the cell cycle and to induce apoptosis in human cell lines. However, since small amounts of the SUV3 helicase were found in the cell nuclei, it was not clear whether the observed phenotypes of SUV3 depletion were of mitochondrial or nuclear origin. In order to answer this question we have designed gene constructs able to inhibit the SUV3 activity exclusively in the cell nuclei. The results indicate that the observed growth rate impairment upon SUV3 depletion is due to its nuclear function(s). Unexpectedly, overexpression of the nuclear-targeted wild-type copies of the SUV3 gene resulted in a higher growth rate. In addition, we demonstrate that the SUV3 helicase can be found in the HeLa cell nucleoli, but it is not detectable in the DNA-repair foci. Our results indicate that the nucleolar-associated human SUV3 protein is an important factor in regulation of the cell cycle.

  20. Regulation of gene expression by the BLM helicase correlates with the presence of G-quadruplex DNA motifs

    DEFF Research Database (Denmark)

    Nguyen, Giang Huong; Tang, Weiliang; Robles, Ana I

    2014-01-01

    Bloom syndrome is a rare autosomal recessive disorder characterized by genetic instability and cancer predisposition, and caused by mutations in the gene encoding the Bloom syndrome, RecQ helicase-like (BLM) protein. To determine whether altered gene expression might be responsible for pathologic...

  1. Molecular architecture of the recombinant human MCM2-7 helicase in complex with nucleotides and DNA

    DEFF Research Database (Denmark)

    Boskovic, Jasminka; Bragado-Nilsson, Elisabeth; Saligram Prabhakar, Bhargav

    2016-01-01

    DNA replication is a key biological process that involves different protein complexes whose assembly is rigorously regulated in a successive order. One of these complexes is a replicative hexameric helicase, the MCM complex, which is essential for the initiation and elongation phases of replicati...

  2. Single molecule measurements of DNA helicase activity with magnetic tweezers and t-test based step-finding analysis

    Science.gov (United States)

    Seol, Yeonee; Strub, Marie-Paule; Neuman, Keir C.

    2016-01-01

    Magnetic tweezers is a versatile and easy to implement single-molecule technique that has become increasingly prevalent in the study of nucleic acid based molecular motors. Here, we provide a description of the magnetic tweezers instrument and guidelines for measuring and analyzing DNA helicase activity. Along with experimental methods, we describe a robust method of single-molecule trajectory analysis based on the Student’s t-test that accommodates continuous transitions in addition to the discrete transitions assumed in most widely employed analysis routines. To illustrate the single-molecule unwinding assay and the analysis routine, we provide DNA unwinding measurements of Escherichia coli RecQ helicase under a variety of conditions (Na+, ATP, temperature, and DNA substrate geometry). These examples reveal that DNA unwinding measurements under various conditions can aid in elucidating the unwinding mechanism of DNA helicase but also emphasize that environmental effects on DNA helicase activity must be considered in relation to in vivo activity and mechanism. PMID:27131595

  3. Ufd1-Npl4 Recruit Cdc48 for Disassembly of Ubiquitylated CMG Helicase at the End of Chromosome Replication

    Directory of Open Access Journals (Sweden)

    Marija Maric

    2017-03-01

    Full Text Available Disassembly of the Cdc45-MCM-GINS (CMG DNA helicase is the key regulated step during DNA replication termination in eukaryotes, involving ubiquitylation of the Mcm7 helicase subunit, leading to a disassembly process that requires the Cdc48 “segregase”. Here, we employ a screen to identify partners of budding yeast Cdc48 that are important for disassembly of ubiquitylated CMG helicase at the end of chromosome replication. We demonstrate that the ubiquitin-binding Ufd1-Npl4 complex recruits Cdc48 to ubiquitylated CMG. Ubiquitylation of CMG in yeast cell extracts is dependent upon lysine 29 of Mcm7, which is the only detectable site of ubiquitylation both in vitro and in vivo (though in vivo other sites can be modified when K29 is mutated. Mutation of K29 abrogates in vitro recruitment of Ufd1-Npl4-Cdc48 to the CMG helicase, supporting a model whereby Ufd1-Npl4 recruits Cdc48 to ubiquitylated CMG at the end of chromosome replication, thereby driving the disassembly reaction.

  4. Acute inactivation of the replicative helicase in human cells triggers MCM8-9-dependent DNA synthesis

    DEFF Research Database (Denmark)

    Natsume, Toyoaki; Nishimura, Kohei; Minocherhomji, Sheroy

    2017-01-01

    stemming from replisome dissociation during DNA replication perturbation, we used a degron-based system for inducible proteolysis of a subunit of the replicative helicase. We show that MCM2-depleted cells activate a DNA damage response pathway and generate replication-associated DNA double-strand breaks...

  5. RNA helicase DDX3 is a regulatory subunit of casein kinase 1 in Wnt-beta-catenin signaling

    NARCIS (Netherlands)

    Cruciat, C.M.; Dolde, C.; de Groot, R.E.; Ohkawara, B.; Reinhard, C.; Korswagen, H.C.; Niehrs, C.

    2013-01-01

    Casein kinase 1 (CK1) members play key roles in numerous biological processes. They are considered "rogue" kinases, because their enzymatic activity appears unregulated. Contrary to this notion, we have identified the DEAD-box RNA helicase DDX3 as a regulator of the Wnt-beta-catenin network, where

  6. Effects of moisture content or particle size on the in situ degradability of maize silage and alfalfa haylage in lactating dairy cows

    OpenAIRE

    Yang Zou; Shuangzhao Dong; Yun Du; Shengli Li; Yajing Wang; Zhijun Cao

    2016-01-01

    A study using four Holstein cows with ruminal cannulas was conducted to evaluate the degradability of different moisture content or particle size of maize silage and alfalfa haylage. The maize silage (MS; 20-mm length) and alfalfa haylage (AH; 40-mm length) samples were wet (wet maize silage, MSW; wet alfalfa haylage, AHW), dried (dried maize silage, MSD; dried alfalfa haylage, AHD), or ground to pass through a 2.5-mm screen (dried ground maize silage, MSG; dried ground alfalfa haylage, AHG)....

  7. Emerging importance of helicases in plant stress tolerance: characterization of Oryza sativa repair helicase XPB2 promoter and its functional validation in tobacco under multiple stresses

    Directory of Open Access Journals (Sweden)

    Shailendra eRaikwar

    2015-12-01

    Full Text Available Genetic material always remains at the risk of spontaneous or induced damage which challenges the normal functioning of DNA molecule, thus, DNA repair is vital to protect the organisms against genetic damage. DNA hHelicases, the unique molecular motors, are emerged as potentialprospective molecules to engineer stress tolerance in plants and are involved in a variety of DNA nucleic acid metabolismc processes including DNA repair. The DNA repair helicase, OsXPB2 is an evolutionary conserved protein present in different organisms, including plants. Availability of few efficient promoters for gene expression in plants provoked us to study the promoter of XPB for better understanding of gene regulation under stress The analysis of promoter sequence from plant genome is important in understanding the gene regulation. Hereconditions. Here, we report the in silico analysis of novel stress inducible promoter of rice Oryza sativa OsXPB2 (OsXPB2. gene is reported. The in vivo validation of functionality/activity of novel stress inducible promoter of rice OsXPB2 gene promoter under abiotic and hormonal stress conditions was performed by Agrobacterium-mediated transient assay in tobacco leaves using OsXPB2::GUS chimeric construct. Our resultsThe present research revealed that OsXPB2 promoter contains cis-elements accounting for various abiotic stresses (salt, dehydration or cold and hormone (Auxin, ABA or MeJA induced GUS expression/activity in the promoter-reporter assay. The promoter region of OsXPB2 contains CACG, GTAACG, CACGTG, CGTCA CCGCCGCGCT cis acting-elements which are reported to be salt, dehydration, cold, MeJA or ABA responsive, respectively. Functional analysis was done by Agrobacterium-transient assays using agroinfiltration in tobacco leaves, followed by GUS staining and fluorescence quantitative analyses. The results revealed high induction of GUS activity under multiple abiotic stresses as compared to mock treated control. The present

  8. Replacement of alfalfa hay (Medicago sativa) with maralfalfahay (Pennisetum sp.) in diets of lactating dairy goats

    DEFF Research Database (Denmark)

    Criscioni, P.; Marti, J.V.; Pérez-Baena, I.

    2016-01-01

    tThe objective of this experiment was to study the effects of substituting alfalfa (Medicagosativa) with maralfalfa (Pennisetum sp.) on energy, nitrogen and carbon balance, methaneemission, and milk performance in dairy goats. Ten Murciano-Granadina dairy goats in latelactation (45.7 ± 2.96 kg...... of body weight [BW]) were selected in a 2-treatment and crossoverdesign experiment where each goat received both treatments in 2 periods. One group offive goats was fed a mixed ration with alfalfa as forage (A diet) and the other diet replacedalfalfa with maralfalfa (M diet) in a forage concentrate ratio...

  9. Evolutionary relationship of alfalfa mosaic virus with cucumber mosaic virus and brome mosaic virus

    OpenAIRE

    Savithri, HS; Murthy, MRN

    1983-01-01

    The amino acid sequences of the non-structural protein (molecular weight 35,000; 3a protein) from three plant viruses - cucumber mosaic, brome mosaic and alfalfa mosaic have been systematically compared using the partial genomic sequences for these three viruses already available. The 3a protein of cucumber mosaic virus has an amino acid sequence homology of 33.7% with the corresponding protein of brome mosaic virus. A similar protein from alfalfa mosaic virus has a homology of 18.2% and 14.2...

  10. Growth Of New Alfalfa And Cocksfoot Shoot S During Water-Deficit And Irrigation .2. Modeling

    International Nuclear Information System (INIS)

    Duru, M.; Langlet, A.

    1995-01-01

    Eight regrowths of alfalfa and thirteen of cocksfoot were compared with and without irrigation and with two levels of nitrogen supply (cocksfoot). Aerial biomass was modellized according to PARa. Following a water shortage, the efficiency of radiation intercepted decreased more frequently than the efficiency of the conversion of radiation in biomass for cocksfoot, but the contrary was observed for alfalfa. The decrease in PARa resulted from the direct effect of water shortage, but also from indirect (low value of herbage nitrogen level) and deferred (after-effect as residual leaf area index) effects [it

  11. Molecular and Functional Characterization of RecD, a Novel Member of the SF1 Family of Helicases, from Mycobacterium tuberculosis.

    Science.gov (United States)

    Dewhare, Shivendra Singh; Umesh, T G; Muniyappa, K

    2015-05-08

    The annotated whole-genome sequence of Mycobacterium tuberculosis revealed the presence of a putative recD gene; however, the biochemical characteristics of its encoded protein product (MtRecD) remain largely unknown. Here, we show that MtRecD exists in solution as a stable homodimer. Protein-DNA binding assays revealed that MtRecD binds efficiently to single-stranded DNA and linear duplexes containing 5' overhangs relative to the 3' overhangs but not to blunt-ended duplex. Furthermore, MtRecD bound more robustly to a variety of Y-shaped DNA structures having ≥18-nucleotide overhangs but not to a similar substrate containing 5-nucleotide overhangs. MtRecD formed more salt-tolerant complexes with Y-shaped structures compared with linear duplex having 3' overhangs. The intrinsic ATPase activity of MtRecD was stimulated by single-stranded DNA. Site-specific mutagenesis of Lys-179 in motif I abolished the ATPase activity of MtRecD. Interestingly, although MtRecD-catalyzed unwinding showed a markedly higher preference for duplex substrates with 5' overhangs, it could also catalyze significant unwinding of substrates containing 3' overhangs. These results support the notion that MtRecD is a bipolar helicase with strong 5' → 3' and weak 3' → 5' unwinding activities. The extent of unwinding of Y-shaped DNA structures was ∼3-fold lower compared with duplexes with 5' overhangs. Notably, direct interaction between MtRecD and its cognate RecA led to inhibition of DNA strand exchange promoted by RecA. Altogether, these studies provide the first detailed characterization of MtRecD and present important insights into the type of DNA structure the enzyme is likely to act upon during the processes of DNA repair or homologous recombination. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. The spreading of Alfalfa mosaic virus in lavandin in Croatia

    Directory of Open Access Journals (Sweden)

    Ivana Stanković

    2014-06-01

    Full Text Available survey was conducted in 2012 and 2013 to detect the presence and distribution of Alfalfa mosaic virus (AMV in lavandin crops growing in continental parts of Croatia. A total of 73 lavandin samples from six crops in different localities were collected and analyzed for the presence of AMV and Cucumber mosaic virus (CMV using commercial double-antibody sandwich (DAS-ELISA kits. AMV was detected serologically in 62 samples collected at three different localities, and none of the samples tested positive for CMV. For further analyses, six selected samples of naturally infected lavandin plants originating from different localities were mechanically transmitted to test plants: Chenopodium quinoa, C. amaranticolor, Nicotiana benthamiana and Ocimum basilicum, confirming the infectious nature of the disease. Molecular detection was performed by amplification of a 751 bp fragment in all tested samples, using the specific primers CP AMV1/CP AMV2 that amplify the part of the coat protein (CP gene and 3’-UTR. The RT-PCR products derived from the isolates 371-13 and 373-13 were sequenced (KJ504107 and KJ504108, respectively and compared with the AMV sequences available in GenBank. CP sequence analysis, conducted using the MEGA5 software, revealed that the isolate 371-13 had the highest nucleotide identity of 99.5% (100% amino acid identity with an isolate from Argentina originating from Medicago sativa (KC881010, while the sequence of isolate 373-13 had the highest identity with an Italian AMV isolate from Lavandula stoechas (FN667967 of 98.6% (99% amino acid identity. Phylogenetic analysis revealed the clustering of selected isolates into four molecular groups and the lavandin AMV isolates from Croatia grouped into two distinct groups, implying a significant variability within the AMV lavandin population.

  13. Evaluation of Selection Indices for Alfalfa (Medicago sativa L.

    Directory of Open Access Journals (Sweden)

    Hassan MONIRIFAR

    2010-03-01

    Full Text Available In order to evaluate the efficiency of selection indices in alfalfa improvement, an experiment was conducted from 2000 to 2007 at East Azarbaijan Agricultural and Natural Resources Research Center, Iran. A set of 29 native ecotypes, which were collected in 2000 and 2001 from Azerbaijan (Iran, together with one improved variety were used to conduct a polycross nursery. For the purpose of random mating, a randomized complete block design was used with 12 replications arranged in this nursery. The resulting 30 half-sib families were planted individually in pots and the 30 days old seedlings were transplanted to the field in May, 2004. Each 3-row plot consisted of 45 HS plants. Several traits, such as individual plants� fresh weight and individual plants� dry weight (IPFW, IPDW, number of shoots per plant (NS and plant height (PH in each harvest and also, days until 10% flowering, the ratio of fresh and dry weight of leaves/plant and size of trifoliate leaves were measured for three cropping seasons. The results of analysis of variance showed large variation among polycross progenies. Six selection indices (Ii with different number of traits at adult plant stage were evaluated. Based on the result of this investigation, if number of shoots and height of adult plant, excluding yield, are recorded, I2 is suggested. If, in addition to fresh yield, height of adult plant is measured, I6 is recommended. I4 is useful when number of shoots and plant height with dry yield are included in the index. In conclusion, the importance of mature plant traits in selection indices was in the order of yield > plant height > number of shoots. The results provided more evidence that selection indices incorporating the component of dry yield are more advantageous. The most efficient selection index consisted of NS, IPDW and PH, having a relative efficiency of 280%.

  14. Thermoperiodism Synchronizes Emergence in the Alfalfa Leafcutting Bee (Hymenoptera: Megachilidae).

    Science.gov (United States)

    Yocum, George D; Rinehart, Joseph P; Yocum, Ian S; Kemp, William P; Greenlee, Kendra J

    2016-02-01

    Alfalfa seed production in the northwestern United States and western Canada is heavily dependent upon the pollinating services of Megachile rotundata (F.) (Hymenoptera: Megachilidae). M. rotundata females nest in cavities either naturally occurring or in artificial nesting blocks. Because of the physical nature of the nest, M. rotundata brood may have limited to no exposure to photoperiodic cues in order to regulate important circadian functions. Therefore, various thermoperiod regimes were used to characterize the possible role of thermoperiodism in synchronizing M. rotundata adult emergence. Adult emergence was monitored using a microprocessor-controlled event logger. Incubating bees under constant 29°C and darkness resulted in an arhythmic adult emergence pattern. Exposing developing M. rotundata to a thermoperiod synchronized emergence to the beginning of the thermophase and decreased the total number of days required for all adults to emerge. The amplitude of the thermoperiod regulated the timing of peak emergence in relationship to the increase in temperature. A thermoperiod amplitude of only 2°C was sufficient to synchronize peak adult emergence to take place during the rise in temperature. Increasing the amplitude of the thermoperiod to 4 or 8°C caused a positively correlated shift in peak emergence to later in the thermophase. Brood stored under constant 29°C and darkness for different durations (May or June early in the growing season or July or August late in the growing season) or under a fluctuating thermal regime (base temperature of 6°C and daily 1-h pulse of 20°C until September or November) maintained their capacity for entraining emergence timing by thermoperiodism. Published by Oxford University Press on behalf of Entomological Society of America 2015. This work is written by US Government employees and is in the public domain in the US.

  15. Ten Putative Contributors to the Obesity Epidemic

    Science.gov (United States)

    McAllister, Emily J.; Dhurandhar, Nikhil V.; Keith, Scott W.; Aronne, Louis J.; Barger, Jamie; Baskin, Monica; Benca, Ruth M.; Biggio, Joseph; Boggiano, Mary M.; Eisenmann, Joe C.; Elobeid, Mai; Fontaine, Kevin R.; Gluckman, Peter; Hanlon, Erin C.; Katzmarzyk, Peter; Pietrobelli, Angelo; Redden, David T.; Ruden, Douglas M.; Wang, Chenxi; Waterland, Robert A.; Wright, Suzanne M.; Allison, David B.

    2010-01-01

    The obesity epidemic is a global issue and shows no signs of abating, while the cause of this epidemic remains unclear. Marketing practices of energy-dense foods and institutionally-driven declines in physical activity are the alleged perpetrators for the epidemic, despite a lack of solid evidence to demonstrate their causal role. While both may contribute to obesity, we call attention to their unquestioned dominance in program funding and public efforts to reduce obesity, and propose several alternative putative contributors that would benefit from equal consideration and attention. Evidence for microorganisms, epigenetics, increasing maternal age, greater fecundity among people with higher adiposity, assortative mating, sleep debt, endocrine disruptors, pharmaceutical iatrogenesis, reduction in variability of ambient temperatures, and intrauterine and intergenerational effects, as contributing factors to the obesity epidemic are reviewed herein. While the evidence is strong for some contributors such as pharmaceutical-induced weight gain, it is still emerging for other reviewed factors. Considering the role of such putative etiological factors of obesity may lead to comprehensive, cause specific, and effective strategies for prevention and treatment of this global epidemic. PMID:19960394

  16. Substrate-assisted mechanism of RNP disruption by the spliceosomal Brr2 RNA helicase

    Science.gov (United States)

    Theuser, Matthias; Höbartner, Claudia; Wahl, Markus C.; Santos, Karine F.

    2016-01-01

    The Brr2 RNA helicase disrupts the U4/U6 di-small nuclear RNA–protein complex (di-snRNP) during spliceosome activation via ATP-driven translocation on the U4 snRNA strand. However, it is unclear how bound proteins influence U4/U6 unwinding, which regions of the U4/U6 duplex the helicase actively unwinds, and whether U4/U6 components are released as individual molecules or as subcomplexes. Here, we set up a recombinant Brr2-mediated U4/U6 di-snRNP disruption system, showing that sequential addition of the U4/U6 proteins small nuclear ribonucleoprotein-associated protein 1 (Snu13), pre-mRNA processing factor 31 (Prp31), and Prp3 to U4/U6 di-snRNA leads to a stepwise decrease of Brr2-mediated U4/U6 unwinding, but that unwinding is largely restored by a Brr2 cofactor, the C-terminal Jab1/MPN domain of the Prp8 protein. Brr2-mediated U4/U6 unwinding was strongly inhibited by mutations in U4/U6 di-snRNAs that diminish the ability of U6 snRNA to adopt an alternative conformation but leave the number and kind of U4/U6 base pairs unchanged. Irrespective of the presence of the cofactor, the helicase segregated a Prp3-Prp31-Snu13-U4/U6 RNP into an intact Prp31-Snu13-U4 snRNA particle, free Prp3, and free U6 snRNA. Together, these observations suggest that Brr2 translocates only a limited distance on the U4 snRNA strand and does not actively release RNA-bound proteins. Unwinding is then completed by the partially displaced U6 snRNA adopting an alternative conformation, which leads to dismantling of the Prp3-binding site on U4/U6 di-snRNA but leaves the Prp31- and Snu13-binding sites on U4 snRNA unaffected. In this fashion, Brr2 can activate the spliceosome by stripping U6 snRNA of all precatalytic binding partners, while minimizing logistic requirements for U4/U6 di-snRNP reassembly after splicing. PMID:27354531

  17. Fixed-Precision Sequential Sampling Plans for Estimating Alfalfa Caterpillar, Colias lesbia, Egg Density in Alfalfa, Medicago sativa, Fields in Córdoba, Argentina

    Science.gov (United States)

    Serra, Gerardo V.; Porta, Norma C. La; Avalos, Susana; Mazzuferi, Vilma

    2013-01-01

    The alfalfa caterpillar, Colias lesbia (Fabricius) (Lepidoptera: Pieridae), is a major pest of alfalfa, Medicago sativa L. (Fabales: Fabaceae), crops in Argentina. Its management is based mainly on chemical control of larvae whenever the larvae exceed the action threshold. To develop and validate fixed-precision sequential sampling plans, an intensive sampling programme for C. lesbia eggs was carried out in two alfalfa plots located in the Province of Córdoba, Argentina, from 1999 to 2002. Using Resampling for Validation of Sampling Plans software, 12 additional independent data sets were used to validate the sequential sampling plan with precision levels of 0.10 and 0.25 (SE/mean), respectively. For a range of mean densities of 0.10 to 8.35 eggs/sample, an average sample size of only 27 and 26 sample units was required to achieve a desired precision level of 0.25 for the sampling plans of Green and Kuno, respectively. As the precision level was increased to 0.10, average sample size increased to 161 and 157 sample units for the sampling plans of Green and Kuno, respectively. We recommend using Green's sequential sampling plan because it is less sensitive to changes in egg density. These sampling plans are a valuable tool for researchers to study population dynamics and to evaluate integrated pest management strategies. PMID:23909840

  18. Silicon Priming Created an Enhanced Tolerance in Alfalfa (Medicago sativa L.) Seedlings in Response to High Alkaline Stress.

    Science.gov (United States)

    Liu, Duo; Liu, Miao; Liu, Xiao-Long; Cheng, Xian-Guo; Liang, Zheng-Wei

    2018-01-01

    Alkaline stress as a result of higher pH usually triggers more severe physiological damage to plants than that of saline stress with a neutral pH. In the present study, we demonstrated that silicon (Si) priming of alfalfa ( Medicago sativa L.) seedlings increased their tolerance to high alkaline stress situations. Gongnong No. 1 seedlings were subjected to alkaline stress simulated by 25 mM Na 2 CO 3 (pH 11.2). Alkaline stress greatly decreased the biomass and caused severe lodging or wilting of alfalfa seedlings. In contrast, the application of Si to alfalfa seedlings 36 h prior to the alkaline treatment significantly alleviated the damage symptoms and greatly increased the biomass and chlorophyll content. Because of being concomitant with increasing photosynthesis and water use efficiency, decreasing membrane injury and malondialdehyde content, and increasing peroxidase and catalase ascorbate activities in alfalfa leaves, thereby alleviating the triggered oxidative damage by alkaline stress to the plant. Furthermore, Si priming significantly decreased the accumulation of protein and proline content in alfalfa, thus reducing photosynthetic feedback repression. Si priming significantly accumulated more Na in the roots, but led to a decrease of Na accumulation and an increase of K accumulation in the leaves under alkaline stress. Meanwhile, Si priming decreased the accumulation of metal ions such as Mg, Fe, Mn, and Zn in the roots of alfalfa seedlings under alkaline stress. Collectively, these results suggested that Si is involved in the metabolic or physiological changes and has a potent priming effect on the alkaline tolerance of alfalfa seedlings. The present study indicated that Si priming is a new approach to improve the alkaline tolerance in alfalfa and provides increasing information for further exploration of the alkaline stress response at the molecular level in alfalfa.

  19. FBH1 helicase disrupts RAD51 filaments in vitro and modulates homologous recombination in mammalian cells

    DEFF Research Database (Denmark)

    Simandlova, Jitka; Zagelbaum, Jennifer; Payne, Miranda J

    2013-01-01

    Efficient repair of DNA double strand breaks and interstrand cross-links requires the homologous recombination (HR) pathway, a potentially error-free process that utilizes a homologous sequence as a repair template. A key player in HR is RAD51, the eukaryotic ortholog of bacterial RecA protein. RAD......51 can polymerize on DNA to form a nucleoprotein filament that facilitates both the search for the homologous DNA sequences and the subsequent DNA strand invasion required to initiate HR. Because of its pivotal role in HR, RAD51 is subject to numerous positive and negative regulatory influences...... filaments on DNA through its ssDNA translocase function. Consistent with this, a mutant mouse embryonic stem cell line with a deletion in the FBH1 helicase domain fails to limit RAD51 chromatin association and shows hyper-recombination. Our data are consistent with FBH1 restraining RAD51 DNA binding under...

  20. RTEL1 is a replisome-associated helicase that promotes telomere and genome-wide replication.

    Science.gov (United States)

    Vannier, Jean-Baptiste; Sandhu, Sumit; Petalcorin, Mark I R; Wu, Xiaoli; Nabi, Zinnatun; Ding, Hao; Boulton, Simon J

    2013-10-11

    Regulator of telomere length 1 (RTEL1) is an essential DNA helicase that disassembles telomere loops (T loops) and suppresses telomere fragility to maintain the integrity of chromosome ends. We established that RTEL1 also associates with the replisome through binding to proliferating cell nuclear antigen (PCNA). Mouse cells disrupted for the RTEL1-PCNA interaction (PIP mutant) exhibited accelerated senescence, replication fork instability, reduced replication fork extension rates, and increased origin usage. Although T-loop disassembly at telomeres was unaffected in the mutant cells, telomere replication was compromised, leading to fragile sites at telomeres. RTEL1-PIP mutant mice were viable, but loss of the RTEL1-PCNA interaction accelerated the onset of tumorigenesis in p53-deficient mice. We propose that RTEL1 plays a critical role in both telomere and genome-wide replication, which is crucial for genetic stability and tumor avoidance.

  1. Association between regulator of telomere elongation helicase1 (RTEL1) gene and HAPE risk

    Science.gov (United States)

    Rong, Hao; He, Xue; Zhu, Linhao; Zhu, Xikai; Kang, Longli; Wang, Li; He, Yongjun; Yuan, Dongya; Jin, Tianbo

    2017-01-01

    Abstract High altitude pulmonary edema (HAPE) is a paradigm of pulmonary edema. Mutations in regulator of telomere elongation helicase1 (RTEL1) represent an important contributor to risk for pulmonary fibrosis. However, little information is found about the association between RTEL1 and HAPE risk. The present study was undertaken to tentatively explore the potential relation between single-nucleotide polymorphisms (SNPs) in RTEL1 and HAPE risk in Chinese Han population. A total of 265 HAPE patients and 303 healthy controls were included in our case-control study. Four SNPs in RTEL1 were selected and genotyped using the Sequenom MassARRAY method. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated by unconditional logistic regression with adjustment for gender and age. All P values were Bonferroni corrected, and statistical significance was set at P RTEL1 and a decreased risk HAPE in the Chinese population. The results need further confirmation. PMID:28953687

  2. Alfalfa interseeded into silage corn can enhance productivity and soil and water conservation

    Science.gov (United States)

    Alfalfa and corn silage are widely planted for dairy forage production systems throughout the northern regions of the USA, accounting for about 0.8 and 1.9 million hectares per year, respectively. Much of this area could benefit from strategies to reduce soil erosion and nutrient losses. Because the...

  3. Study on Effect of alfalfa, ryegrass and wheat middlings contents in ...

    African Journals Online (AJOL)

    微软用户

    2013-03-13

    Mar 13, 2013 ... 3Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, People's Republic of China. Accepted 16 ... The body weight (BW) of Group 3 geese was the biggest ... of alfalfa, ryegrass and wheat bran in diet in geese was 18%. .... images of tissues were taken using a Nikon Optiphot microscope.

  4. First report of Alfalfa mosaic virus infecting basil (Ocimum basilicum L.) in California.

    Science.gov (United States)

    Basil (Ocimum basilicum L.) plants collected from a field in Imperial County, CA in May, 2011 were found to exhibit yellowing, chlorotic sectors and spots on leaves, resulting in plants being unmarketable. Total nucleic acid was extracted from plants and tested by RT-PCR for the presence of Alfalfa...

  5. Soil sulfur amendments suppress Selenium uptake by alfalfa and western wheatgrass

    Science.gov (United States)

    C. L. Mackowiak; M. C. Amacher

    2008-01-01

    Selenium (Se) is a potential soil contaminant in many parts of the world where it can pose a health risk to livestock and wildlife. Phosphate ore mining in Southeast Idaho has resulted in numerous waste rock dumps revegetated with forages to stabilize the dumps and support grazing. Alfalfa (Medicago sativa L.), smooth brome (Bromus inermis...

  6. The effects of alfalfa particle size and acid treated protein on ruminal ...

    African Journals Online (AJOL)

    This study was conducted to investigate the effects of alfalfa particle size (long vs. fine) and canola meal treated with hydrochloric acid solution (untreated vs treated) on ruminal chemical composition, liquid, particulate, escapable and non escapable phases in Zel sheep. Four ruminally cannulated sheep received a mixed ...

  7. Association Mapping of Biomass Yield and Stem Composition in a Tetraploid Alfalfa Breeding Population

    Directory of Open Access Journals (Sweden)

    Xuehui Li

    2011-03-01

    Full Text Available Alfalfa ( L., an important forage crop that is also a potential biofuel crop, has advantages of high yield, high lignocellulose concentration in stems, and has low input costs. In this study, we investigated population structure and linkage disequilibrium (LD patterns in a tetraploid alfalfa breeding population using genome-wide simple sequence repeat (SSR markers and identified markers related to yield and cell wall composition by association mapping. No obvious population structure was found in our alfalfa breeding population, which could be due to the relatively narrow genetic base of the founders and/or due to two generations of random mating. We found significant LD ( 10% alleles across the 71 SSR markers, 15 showed strong association ( < 0.005 with yield in at least one of five environments, and most of the 15 alleles were identified in multiple environments. Only one allele showed strong association with acid detergent fiber (ADF and one allele with acid detergent lignin (ADL. Alleles associated with traits could be directly applied in a breeding program using marker-assisted selection. However, based on our estimated LD level, we would need about 1000 markers to explore the whole alfalfa genome for association between markers and traits.

  8. Critical PO2 of developing Megachile rotundata, the alfalfa leaf-cutting bee

    Science.gov (United States)

    The alfalfa leaf-cutting bee, Megachile rotundata, is a solitary, cavity-nesting bee. Juvenile bees develop inside brood cells constructed out of leaf pieces. During development inside the brood cell, pre-pupae may experience hypoxic conditions from both the cavity nesting behavior and brood cell ...

  9. Best Phd thesis Prize : Statistical analysis of ALFALFA galaxies: insights in galaxy

    NARCIS (Netherlands)

    Papastergis, E.

    We use the rich dataset of local universe galaxies detected by the ALFALFA 21cm survey to study the statistical properties of gas-bearing galaxies. In particular, we measure the number density of galaxies as a function of their baryonic mass ("baryonic mass function") and rotational velocity

  10. Crop mergers: Management of soil contamination and leaf loss in alfalfa

    Science.gov (United States)

    Maximizing the capacity and subsequent efficiency of the forage harvester necessitates consolidation (raking or merging) of alfalfa cuttings. Although rotary rakes are in wide use, the use of continuous pickup belt mergers is increasing in the Midwestern U.S. Previous work on crop consolidation is l...

  11. Effect of space flight factors on alfalfa seeds | Ren | African Journal ...

    African Journals Online (AJOL)

    Abstract. To explore the effect of space flight factors on the early development of alfalfa seedling, dry seeds were placed onboard a satellite for a 15-day flight. After retrieval, the ultra structure of seed coat and the chemical content of seed were tested, followed by tests for germinate ability, seedling growth, and mitotic and ...

  12. Soil water distribution on different number of growing years of alfalfa ...

    African Journals Online (AJOL)

    GREGORY

    2010-08-30

    Aug 30, 2010 ... dNational Engineering Research Center for Water-Saving and ... After alfalfa grew for >18 years, the annual recovery of its soil water at 0 - 200 cm soil depth was 1.49%, ... yield of following crops, or even lead to failure of the.

  13. Milk production response to feeding alfalfa silage inoculated with Lactobacillus plantarum

    Science.gov (United States)

    In mini-silo trials, silages treated with a Lactobacillus plantarum silage inoculant (Ecosyl, Yorkshire, UK) had increased in vitro rumen microbial biomass production compared to untreated. Our objective was to determine if alfalfa silage treated with this inoculant could produce a milk production r...

  14. Estimation of the genetic diversity in tetraploid alfalfa populations based on RAPD markers for breeding purposes.

    Science.gov (United States)

    Nagl, Nevena; Taski-Ajdukovic, Ksenija; Barac, Goran; Baburski, Aleksandar; Seccareccia, Ivana; Milic, Dragan; Katic, Slobodan

    2011-01-01

    Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon's information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA) showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm.

  15. Uptake of oxytetracycline and its phytotoxicity to alfalfa (Medicago sativa L.)

    Energy Technology Data Exchange (ETDEWEB)

    Kong, W D [Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 (China); Zhu, Y G [Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 (China); Liang, Y C [Ministry of Agriculture Key Laboratory of Plant Nutrition and Nutrient Cycling, Institute of Soils and Fertilizers, Chinese Academy of Agricultural Sciences, Beijing 100081 (China); Zhang, J [Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 (China); Smith, F A [Soil and Land Systems, School of Earth and Environmental Sciences, University of Adelaide, DP 636, Adelaide, SA 5005 (Australia); Yang, M [Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 (China)

    2007-05-15

    A series of experiments were conducted in a hydroponic system to investigate the uptake of oxytetracycline (OTC) and its toxicity to alfalfa (Medicago sativa L.). OTC inhibited alfalfa shoot and root growth by up to 61% and 85%, respectively. The kinetics of OTC uptake could be well described by Michaelis-Menten equation with V {sub max} of 2.25 {mu}mol g{sup -1} fresh weight h{sup -1}, and K {sub m} of 0.036 mM. The uptake of OTC by alfalfa was strongly inhibited by the metabolic inhibitor, 2,4-DNP (2,4-dinitrophenol), at pH 3.5 and 6.0, but not by the aquaporin competitors, glycerol and Ag{sup +}. OTC uptake, however, was significantly inhibited by Hg{sup 2+}, suggesting that the inhibition of influx was due to general cellular stress rather than the specific action of Hg{sup 2+} on aquaporins. Results from the present study suggested that OTC uptake into alfalfa is an energy-dependent process. - Plant uptake of antibiotic oxytetracycline is energy-dependent.

  16. Uptake of oxytetracycline and its phytotoxicity to alfalfa (Medicago sativa L.)

    International Nuclear Information System (INIS)

    Kong, W.D.; Zhu, Y.G.; Liang, Y.C.; Zhang, J.; Smith, F.A.; Yang, M.

    2007-01-01

    A series of experiments were conducted in a hydroponic system to investigate the uptake of oxytetracycline (OTC) and its toxicity to alfalfa (Medicago sativa L.). OTC inhibited alfalfa shoot and root growth by up to 61% and 85%, respectively. The kinetics of OTC uptake could be well described by Michaelis-Menten equation with V max of 2.25 μmol g -1 fresh weight h -1 , and K m of 0.036 mM. The uptake of OTC by alfalfa was strongly inhibited by the metabolic inhibitor, 2,4-DNP (2,4-dinitrophenol), at pH 3.5 and 6.0, but not by the aquaporin competitors, glycerol and Ag + . OTC uptake, however, was significantly inhibited by Hg 2+ , suggesting that the inhibition of influx was due to general cellular stress rather than the specific action of Hg 2+ on aquaporins. Results from the present study suggested that OTC uptake into alfalfa is an energy-dependent process. - Plant uptake of antibiotic oxytetracycline is energy-dependent

  17. Correlation of fermentation characteristics with intake and digestibility of alfalfa silage in gestating ewes

    Science.gov (United States)

    Baled silage production provides benefits to farmers because it reduces leaf losses, and requires a shorter wilting time, thereby limiting risks of exposure to rain compared with making hay. Our objective was to investigate the correlation of alfalfa silage fermentation parameters with intake and di...

  18. cis-acting elements involved in replication of alfalfa mosaic virus RNAs in vitro

    NARCIS (Netherlands)

    van der Kuyl, A. C.; Langereis, K.; Houwing, C. J.; Jaspars, E. M.; Bol, J. F.

    1990-01-01

    A DNA copy of alfalfa mosaic virus (AIMV) RNA3 was transcribed in vitro in two different orientations with T7 RNA polymerase and the transcripts were used as templates for a virus-specific RNA-dependent RNA polymerase (RdRp) purified from AIMV-infected bean plants. Minus-stranded templates were

  19. Boosting Alfalfa (Medicago sativa L. Production With Rhizobacteria From Various Plants in Saudi Arabia

    Directory of Open Access Journals (Sweden)

    Ihsanullah Daur

    2018-04-01

    Full Text Available This study focused on rhizobacteria to promote sustainable crop production in arid regions of Saudi Arabia. The study isolated 17 tightly root-adhering rhizobacteria from various plants at Hada Al Sham in Saudi Arabia. All 17 rhizobacterial isolates were confirmed as plant growth promoting rhizobacteria by classical biochemical tests. Using 16S rDNA gene sequence analyses, the strains were identified as Bacillus, Acinetobacter and Enterobacter. Subsequently, the strains were assessed for their ability to improve the physiology, nutrient uptake, growth, and yield of alfalfa plants grown under desert agriculture conditions. The field trials were conducted in a randomized complete block design. Inoculation of alfalfa with any of these 17 strains improved the relative water content; chlorophyll a; chlorophyll b; carotenoid contents; nitrogen (N, phosphorus, and potassium contents; plant height; leaf-to-stem ratio; and fresh and dry weight. Acinetobacter pittii JD-14 was most effective to increase fresh and dry weight of alfalfa by 41 and 34%, respectively, when compared to non-inoculated control plants. Nevertheless, all strains enhanced crop traits when compared to controls plants, indicating that these desert rhizobacterial strains could be used to develop an eco-friendly biofertilizer for alfalfa and possibly other crop plants to enhance sustainable production in arid regions.

  20. Role of alfalfa mosaic virus coat protein gene in symptom formation

    NARCIS (Netherlands)

    Neeleman, L.; van der Kuyl, A. C.; Bol, J. F.

    1991-01-01

    On Samsun NN tobacco plants strains 425 and YSMV of alfalfa mosaic virus (AIMV) cause mild chlorosis and local necrotic lesions, respectively. DNA copies of RNA3 of both strains were transcribed in vitro into infectious RNA molecules. When the 425 and YSMV transcripts were inoculated to tobacco

  1. Alfalfa contains substantial 9-hydroperoxide lyase activity and a 3Z:2E-enal isomerase

    NARCIS (Netherlands)

    Vliegenthart, J.F.G.; Noordermeer, M.A.; Veldink, G.A.

    1999-01-01

    Fatty acid hydroperoxides formed by lipoxygenase can be cleaved by hydroperoxide lyase resulting in the formation of short-chain aldehydes and omega-oxo acids. Plant hydroperoxide lyases use 13- or 9-hydroperoxy linoleic and linolenic acid as substrates. Alfalfa (Medicago sativa L.) has been

  2. Study of the boron distribution in pea and alfalfa plants using SSNTD

    International Nuclear Information System (INIS)

    Li Jianming; Inst. for Application of Atomic Energy)" data-affiliation=" (Chinese Academy of Agricultural Sciences, Beijing, BJ (China)> Inst. for Application of Atomic Energy)" >Deng Hongmin

    1988-01-01

    The distribution of boron in pea (Pisum sativum L.) and alfalfa (Medicago sativa L.) was determined by using SSNTD. The results show that boron concentrations in leaves are highest, furthermore boron concentrations of the base leaves are higher than those of the top leaves. Among flower tissues, calyx has the highest boron concentration

  3. Characterizing thermal performance of an important pollinator, the alfalfa leafcutting bee Megachile rotundata

    Science.gov (United States)

    The alfalfa leafcutting bee, Megachile rotundata, undergoes metamorphosis in the spring when temperatures can be highly variable. It is unknown how cold tolerance varies across metamorphosis. We found earlier stages were more tolerant to cold exposure than later stages. Furthermore, we found exposur...

  4. Prohexadione-calcium rate and timing effects on alfalfa interseeded into silage corn

    Science.gov (United States)

    Prohexadione-Ca (PHD) can enhance establishment of alfalfa (Medicago sativa, L.) interseeded into silage corn (Zea mays, L.), but optimal application rates and timing for this growth regulator are unknown. Two experiments examined how single or split applications of 0.25 to 1.0 kg a.i. ha-1 of PHD o...

  5. Development of simple sequence repeat markers and diversity analysis in alfalfa (Medicago sativa L.).

    Science.gov (United States)

    Wang, Zan; Yan, Hongwei; Fu, Xinnian; Li, Xuehui; Gao, Hongwen

    2013-04-01

    Efficient and robust molecular markers are essential for molecular breeding in plant. Compared to dominant and bi-allelic markers, multiple alleles of simple sequence repeat (SSR) markers are particularly informative and superior in genetic linkage map and QTL mapping in autotetraploid species like alfalfa. The objective of this study was to enrich SSR markers directly from alfalfa expressed sequence tags (ESTs). A total of 12,371 alfalfa ESTs were retrieved from the National Center for Biotechnology Information. Total 774 SSR-containing ESTs were identified from 716 ESTs. On average, one SSR was found per 7.7 kb of EST sequences. Tri-nucleotide repeats (48.8 %) was the most abundant motif type, followed by di-(26.1 %), tetra-(11.5 %), penta-(9.7 %), and hexanucleotide (3.9 %). One hundred EST-SSR primer pairs were successfully designed and 29 exhibited polymorphism among 28 alfalfa accessions. The allele number per marker ranged from two to 21 with an average of 6.8. The PIC values ranged from 0.195 to 0.896 with an average of 0.608, indicating a high level of polymorphism of the EST-SSR markers. Based on the 29 EST-SSR markers, assessment of genetic diversity was conducted and found that Medicago sativa ssp. sativa was clearly different from the other subspecies. The high transferability of those EST-SSR markers was also found for relative species.

  6. ALFALFA and WSRT Imaging of Extended H I Features in the Leo Cloud of Galaxies

    NARCIS (Netherlands)

    Leisman, Lukas; Haynes, Martha P.; Giovanelli, Riccardo; Józsa, Gyula; Adams, Elizabeth A. K.; Hess, Kelley M.

    2016-01-01

    We present Arecibo Legacy Fast ALFA (ALFALFA) H I observations of a well-studied region of the Leo Cloud, which includes the NGC 3227 group and the NGC 3190 group. We detect optically dark H I tails and plumes with extents potentially exceeding 600 kpc, well beyond the field of view of previous

  7. Sub-lethal effects of neonicitinoids on the alfalfa leafcutter bee, Megachile rotundata

    Science.gov (United States)

    Neonicotinoids are commonly used pesticides in U.S. agriculture. For many beneficial insect species, lethal effects of neonicotinoids are well-documented; however, much less is known about sublethal exposure. The alfalfa leaf cutter bee Megachile rotundata is a managed pollinator that constructs com...

  8. Tubule-forming capacity of the movement proteins of alfalfa mosaic virus and brome mosaic virus

    NARCIS (Netherlands)

    Kasteel, D. T.; van der Wel, N. N.; Jansen, K. A.; Goldbach, R. W.; van Lent, J. W.

    1997-01-01

    The structural phenotype of the movement proteins (MPs) of two representatives of the Bromoviridae, alfalfa mosaic virus (AMV) and brome mosaic virus (BMV), was studied in protoplasts. Immunofluorescence microscopy showed that the MPs of these viruses, for which there has been no evidence of a

  9. Potential of plant growth regulator and chlormequat chloride on alfalfa seed components

    International Nuclear Information System (INIS)

    Chen, J. S.; Lin, H.; Han, W.

    2016-01-01

    The use of plant growth regulators (PGRs) has opened new prospects for increased seed production in grasses and legumes, but little information is available on the effects of PGRs combination with chlormequat chloride (CCC) on alfalfa (Medicago sativa L.) seed yield components. This study was conducted to evaluate the effects of applying chlormequat chloride in combination with three PGRs (Naphthylacetic acid (NAA), gibberellic acid 3 (GA), and brassinolide (BR)) on seed yield, aboveground biomass, plant height, lodging, yield components. CCC was applied annually at the stooling stage while three PGRs were applied twice each year at the stages of flower bud formation and peak flowering. Results provides evidence that: (i) each PGR consistently increased seed yields, and the numbers of seeds per stem compared to untreated plants; (ii) CCC treatment reduced plant height and lodging, but also significantly decreased seed yield and did not affect aboveground biomass. (iii) effectiveness of CCC application depends on climatic conditions, especially in North-east China. (iiii) the optimum combination of CCC with a PGR to increase alfalfa seed production was failed to identify. (iiiii) no interactions between PGRs and CCC on seed yield were observed and neither the PGRs nor the CCC. But alfalfa seed yield could be improved by combining a PGR such as NAA. Our Results suggest that these PGRs could be used in alfalfa breeding to increase seed yield while maintaining high seed quality. (author)

  10. Isolation, taxonomic analysis, and phenotypic characterization of bacterial endophytes present in alfalfa (Medicago sativa) seeds.

    Science.gov (United States)

    López, José Luis; Alvarez, Florencia; Príncipe, Analía; Salas, María Eugenia; Lozano, Mauricio Javier; Draghi, Walter Omar; Jofré, Edgardo; Lagares, Antonio

    2018-02-10

    A growing body of evidence has reinforced the central role of microbiomes in the life of sound multicellular eukaryotes, thus more properly described as true holobionts. Though soil was considered a main source of plant microbiomes, seeds have been shown to be endophytically colonized by microorganisms thus representing natural carriers of a selected microbial inoculum to the young seedlings. In this work we have investigated the type of culturable endophytic bacteria that are carried within surface-sterilized alfalfa seeds. MALDI-TOF analysis revealed the presence of bacteria that belonged to 40 separate genera, distributed within four taxa (Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes). Nonsymbiotic members of the Rhizobiaceae family were also found. The evaluation of nine different in-vitro biochemical activities demonstrated isolates with complex combinations of traits that, upon a Principal-Component-Analysis, could be classified into four phenotypic groups. That isolates from nearly half of the genera identified had been able to colonize alfalfa plants grown under axenic conditions was remarkable. Further analyses should be addressed to investigating the colonization mechanisms of the alfalfa seeds, the evolutionary significance of the alfalfa-seed endophytes, and also how after germination the seed microbiome competes with spermospheric and rhizospheric soil bacteria to colonize newly emerging seedlings. Copyright © 2018 Elsevier B.V. All rights reserved.

  11. Complementation and recombination between alfalfa mosaic virus RNA3 mutants in tobacco plants

    NARCIS (Netherlands)

    van der Kuyl, A. C.; Neeleman, L.; Bol, J. F.

    1991-01-01

    Deletions were made in an infectious cDNA clone of alfalfa mosaic virus (AIMV) RNA3 and the replication of RNA transcripts of these cDNAs was studied in tobacco plants transformed with AIMV replicase genes (P12 plants). Previously, we found that deletions in the P3 gene did not affect accumulation

  12. Evaluation of subsurface drip irrigation design and management parameters for alfalfa

    NARCIS (Netherlands)

    Kandelous, M.M.; Kamai, T.; Vrugt, J.A.; Šimůnek, J.; Hanson, B.; Hopmans, J.W.

    2012-01-01

    Alfalfa is one of the most cultivated crops in the US, and is being used as livestock feed for the dairy, beef, and horse industries. About nine percent of that is grown in California, yet there is an increasing concern about the large amounts of irrigation water required to attain maximum yield. We

  13. Intracellular localization and movement phenotypes of alfalfa mosaic virus movement protein mutants

    NARCIS (Netherlands)

    Huang, M.; Jongejan, L.; Zheng, H.; Zhang, L.; Bol, J. F.

    2001-01-01

    Thirteen mutations were introduced in the movement protein (MP) gene of Alfalfa mosaic virus (AMV) fused to the green fluorescent protein (GFP) gene and the mutant MP-GFP fusions were expressed transiently in tobacco protoplasts, tobacco suspension cells, and epidermal cells of tobacco leaves. In

  14. Variances in nutrient content and yield of alfalfa protein concentrate processed with five methods

    Science.gov (United States)

    The demand for protein is growing with increased populations and world affluence. A sustainable and affordable protein source is needed to support the growing aquaculture industry worldwide. Alfalfa produces high levels of protein and provides numerous environmental services, potentially making it a...

  15. Circadian entrainment of emerging alfalfa leafcutting bees, Megachile rotundata (Hymenoptera: Megachilidae) to thermoperiodic cues

    Science.gov (United States)

    Emerging insects rely on external cues to synchronize themselves with the environment. Thermoperiod has been identified as an important cue and may be important for insects that emerge from light-restricted habitats. The alfalfa leafcutting bee, Megachile rotundata, a cavity-nesting bee, undergoes d...

  16. Selective lignin downregulation leads to constitutive defense response expression in alfalfa (Medicago sativa L.).

    Science.gov (United States)

    Gallego-Giraldo, Lina; Jikumaru, Yusuke; Kamiya, Yuji; Tang, Yuhong; Dixon, Richard A

    2011-05-01

    • Downregulation of hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase (HCT) in alfalfa (Medicago sativa) reduces lignin levels and improves forage quality and saccharification efficiency for bioethanol production. However, the plants have reduced stature. It was previously reported that HCT-down-regulated Arabidopsis have impaired auxin transport, but this has recently been disproved. • To address the basis for the phenotypes of lignin-modified alfalfa, we measured auxin transport, profiled a range of metabolites including flavonoids and hormones, and performed in depth transcriptome analyses. • Auxin transport is unaffected in HCT antisense alfalfa despite increased flavonoid biosynthesis. The plants show increased cytokinin and reduced auxin levels, and gibberellin levels and sensitivity are both reduced. Levels of salicylic, jasmonic and abscisic acids are elevated, associated with massive upregulation of pathogenesis and abiotic stress-related genes and enhanced tolerance to fungal infection and drought. • We suggest that HCT downregulated alfalfa plants exhibit constitutive activation of defense responses, triggered by release of bioactive cell wall fragments and production of hydrogen peroxide as a result of impaired secondary cell wall integrity. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.

  17. The movement protein and coat protein of alfalfa mosaic virus accumulate in structurally modified plasmodesmata

    NARCIS (Netherlands)

    van der Wel, N. N.; Goldbach, R. W.; van Lent, J. W.

    1998-01-01

    In systemically infected tissues of Nicotiana benthamiana, alfalfa mosaic virus (AMV) coat protein (CP) and movement protein (MP) are detected in plasmodesmata in a layer of three to four cells at the progressing front of infection. Besides the presence of these viral proteins, the plasmodesmata are

  18. Using microcontrollers to study emergence rhythms of the alfalfa leafcutting bee, Megachile rotundata

    Science.gov (United States)

    An important aspect of pollination is phenological overlap of natural events, such as peak flower bloom coinciding with pollinator emergence. Pollinator emergence can be impacted by environmental cues that inform their internal clocks. The alfalfa leafcutting bee, Megachile rotundata is a solitary, ...

  19. Bacterial population dynamics during the ensiling of Medicago sativa (alfalfa) and subsequent exposure to air.

    Science.gov (United States)

    McGarvey, J A; Franco, R B; Palumbo, J D; Hnasko, R; Stanker, L; Mitloehner, F M

    2013-06-01

    To describe, at high resolution, the bacterial population dynamics and chemical transformations during the ensiling of alfalfa and subsequent exposure to air. Samples of alfalfa, ensiled alfalfa and silage exposed to air were collected and their bacterial population structures compared using 16S rRNA gene libraries containing approximately 1900 sequences each. Cultural and chemical analyses were also performed to complement the 16S gene sequence data. Sequence analysis revealed significant differences (P alfalfa-derived library contained mostly sequences associated with the Gammaproteobacteria (including the genera: Enterobacter, Erwinia and Pantoea); the ensiled material contained mostly sequences associated with the lactic acid bacteria (LAB) (including the genera: Lactobacillus, Pediococcus and Lactococcus). Exposure to air resulted in even greater percentages of LAB, especially among the genus Lactobacillus, and a significant drop in bacterial diversity. In-depth 16S rRNA gene sequence analysis revealed significant bacterial population structure changes during ensiling and again during exposure to air. This in-depth description of the bacterial population dynamics that occurred during ensiling and simulated feed out expands our knowledge of these processes. © 2013 The Society for Applied Microbiology No claim to US Government works.

  20. Boosting Alfalfa (Medicago sativa L.) Production With Rhizobacteria From Various Plants in Saudi Arabia

    KAUST Repository

    Daur, Ihsanullah

    2018-04-04

    This study focused on rhizobacteria to promote sustainable crop production in arid regions of Saudi Arabia. The study isolated 17 tightly root-adhering rhizobacteria from various plants at Hada Al Sham in Saudi Arabia. All 17 rhizobacterial isolates were confirmed as plant growth promoting rhizobacteria by classical biochemical tests. Using 16S rDNA gene sequence analyses, the strains were identified as Bacillus, Acinetobacter and Enterobacter. Subsequently, the strains were assessed for their ability to improve the physiology, nutrient uptake, growth, and yield of alfalfa plants grown under desert agriculture conditions. The field trials were conducted in a randomized complete block design. Inoculation of alfalfa with any of these 17 strains improved the relative water content; chlorophyll a; chlorophyll b; carotenoid contents; nitrogen (N), phosphorus, and potassium contents; plant height; leaf-to-stem ratio; and fresh and dry weight. Acinetobacter pittii JD-14 was most effective to increase fresh and dry weight of alfalfa by 41 and 34%, respectively, when compared to non-inoculated control plants. Nevertheless, all strains enhanced crop traits when compared to controls plants, indicating that these desert rhizobacterial strains could be used to develop an eco-friendly biofertilizer for alfalfa and possibly other crop plants to enhance sustainable production in arid regions.

  1. Boosting Alfalfa (Medicago sativa L.) Production With Rhizobacteria From Various Plants in Saudi Arabia

    KAUST Repository

    Daur, Ihsanullah; Saad, Maged; Eida, Abdul Aziz; Ahmad, Shakeel; Shah, Zahid Hussain; Ihsan, Muhammad Z.; Muhammad, Yasir; Sohrab, Sayed S.; Hirt, Heribert

    2018-01-01

    This study focused on rhizobacteria to promote sustainable crop production in arid regions of Saudi Arabia. The study isolated 17 tightly root-adhering rhizobacteria from various plants at Hada Al Sham in Saudi Arabia. All 17 rhizobacterial isolates were confirmed as plant growth promoting rhizobacteria by classical biochemical tests. Using 16S rDNA gene sequence analyses, the strains were identified as Bacillus, Acinetobacter and Enterobacter. Subsequently, the strains were assessed for their ability to improve the physiology, nutrient uptake, growth, and yield of alfalfa plants grown under desert agriculture conditions. The field trials were conducted in a randomized complete block design. Inoculation of alfalfa with any of these 17 strains improved the relative water content; chlorophyll a; chlorophyll b; carotenoid contents; nitrogen (N), phosphorus, and potassium contents; plant height; leaf-to-stem ratio; and fresh and dry weight. Acinetobacter pittii JD-14 was most effective to increase fresh and dry weight of alfalfa by 41 and 34%, respectively, when compared to non-inoculated control plants. Nevertheless, all strains enhanced crop traits when compared to controls plants, indicating that these desert rhizobacterial strains could be used to develop an eco-friendly biofertilizer for alfalfa and possibly other crop plants to enhance sustainable production in arid regions.

  2. Fiber length and pulping characteristics of switchgrass, alfalfa stems, hybrid poplar and willow biomasses.

    Science.gov (United States)

    Ai, Jun; Tschirner, Ulrike

    2010-01-01

    Switchgrass (Panicum virgatum), alfalfa stems (Medicago sativa), second year growth hybrid poplar (Populus) and willow (Salix spp.) were examined to determine fiber characteristics, pulping behavior and paper properties. Alfalfa stems and switchgrass both showed length weighted average fiber length (LWW) of 0.78 mm, a very narrow fiber length distribution and high fines content. Willow and hybrid poplar have lower fines content but a very low average fiber length (0.42 and 0.48 mm LWW). In addition, the four biomass species showed distinctly different chemical compositions. Switchgrass was defibered successfully using Soda and Soda Anthraquinone (AQ) pulping and demonstrated good paper properties. Both fast-growing wood species pulped well using the Kraft process, and showed acceptable tensile strength, but low tear strength. Alfalfa stems reacted very poorly to Soda and Soda AQ pulping but responded well to Kraft and Kraft AQ. Pulps with tensile and tear strength considerably higher than those found for commercial aspen pulps were observed for alfalfa. All four biomass species examined demonstrated low pulp yield. The highest yields were obtained with poplar and switchgrass (around 43%). Considering the short fibers and low yields, all four biomass types will likely only be used in paper manufacturing if they offer considerable economic advantage over traditional pulp wood.

  3. Boosting Alfalfa (Medicago sativa L.) Production With Rhizobacteria From Various Plants in Saudi Arabia.

    Science.gov (United States)

    Daur, Ihsanullah; Saad, Maged M; Eida, Abdul Aziz; Ahmad, Shakeel; Shah, Zahid Hussain; Ihsan, Muhammad Z; Muhammad, Yasir; Sohrab, Sayed S; Hirt, Heribert

    2018-01-01

    This study focused on rhizobacteria to promote sustainable crop production in arid regions of Saudi Arabia. The study isolated 17 tightly root-adhering rhizobacteria from various plants at Hada Al Sham in Saudi Arabia. All 17 rhizobacterial isolates were confirmed as plant growth promoting rhizobacteria by classical biochemical tests. Using 16S rDNA gene sequence analyses, the strains were identified as Bacillus, Acinetobacter and Enterobacter . Subsequently, the strains were assessed for their ability to improve the physiology, nutrient uptake, growth, and yield of alfalfa plants grown under desert agriculture conditions. The field trials were conducted in a randomized complete block design. Inoculation of alfalfa with any of these 17 strains improved the relative water content; chlorophyll a; chlorophyll b; carotenoid contents; nitrogen (N), phosphorus, and potassium contents; plant height; leaf-to-stem ratio; and fresh and dry weight. Acinetobacter pittii JD-14 was most effective to increase fresh and dry weight of alfalfa by 41 and 34%, respectively, when compared to non-inoculated control plants. Nevertheless, all strains enhanced crop traits when compared to controls plants, indicating that these desert rhizobacterial strains could be used to develop an eco-friendly biofertilizer for alfalfa and possibly other crop plants to enhance sustainable production in arid regions.

  4. The effects of perennial ryegrass and alfalfa on microbial abundance and diversity in petroleum contaminated soil

    International Nuclear Information System (INIS)

    Kirk, Jennifer L.; Klironomos, John N.; Lee, Hung; Trevors, Jack T.

    2005-01-01

    Enhanced rhizosphere degradation uses plants to stimulate the rhizosphere microbial community to degrade organic contaminants. We measured changes in microbial communities caused by the addition of two species of plants in a soil contaminated with 31,000 ppm of total petroleum hydrocarbons. Perennial ryegrass and/or alfalfa increased the number of rhizosphere bacteria in the hydrocarbon-contaminated soil. These plants also increased the number of bacteria capable of petroleum degradation as estimated by the most probable number (MPN) method. Eco-Biolog plates did not detect changes in metabolic diversity between bulk and rhizosphere samples but denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified partial 16S rDNA sequences indicated a shift in the bacterial community in the rhizosphere samples. Dice coefficient matrices derived from DGGE profiles showed similarities between the rhizospheres of alfalfa and perennial ryegrass/alfalfa mixture in the contaminated soil at week seven. Perennial ryegrass and perennial ryegrass/alfalfa mixture caused the greatest change in the rhizosphere bacterial community as determined by DGGE analysis. We concluded that plants altered the microbial population; these changes were plant-specific and could contribute to degradation of petroleum hydrocarbons in contaminated soil. - Plant-specific changes in microbial populations on roots affect degradation of petroleum hydrocarbons in contaminated soil

  5. Evaluating Headline fungicide on alfalfa production and sensitivity of pathogens to pyraclostrobin

    Science.gov (United States)

    Headline fungicide was recently registered for management of foliar diseases on alfalfa. The effect of disease control on yield, forage quality, and potential return on investment for fungicide application was determined for field experiments conducted at five locations in 2012, three in Wisconsin a...

  6. Meat goat kids finished on alfalfa, red clover, or orchardgrass pastures: Carcass merit and meat quality

    Science.gov (United States)

    This experiment was conducted in 2005-2007 to evaluate carcass and meat quality parameters when meat goat kids were finished on alfalfa (Medicago sativa L; ALF); red clover (Trifolium pretense L.; RCG); or orchardgrass (Dactylis glomerata L; OGR) pastures. Final shrunk body weights were similar whe...

  7. Polychlorinated biphenyls in alfalfa: Accumulation, sorption and speciation in different plant parts.

    Science.gov (United States)

    Teng, Ying; Sun, Xianghui; Zhu, Lingjia; Christie, Peter; Luo, Yongming

    2017-08-03

    The accumulation, chemical speciation and distribution of polychlorinated biphenyls (PCBs) were investigated in various parts of alfalfa. Moreover, the adsorption characteristics for PCB 28 by alfalfa and the influencing factors of the adsorption characteristics were studied. There were different degrees of PCB accumulation in alfalfa roots, root nodules and shoots. The decreasing order of the accumulation of PCBs in plant tissues was root nodules > roots > shoots, and the decreasing order of the total PCB contents was roots > shoots > root nodules, indicating that the roots were the main sink for PCB accumulation. There were three modes of PCB speciation in alfalfa roots and root nodules, comprising strong sorption (78%) and weak sorption (19%) on tissue surfaces and absorption within tissues (2%). The adsorption isotherms of PCB 28 indicate that the adsorption capacities of root nodules and shoots were both significantly higher than that of the roots. Both lipids and carbohydrates, and especially lipids, affected the PCB adsorption capacities of the tissues. These results may help in the elucidation of the mechanisms of sorption and accumulation of PCBs in the plants and their main influencing factors and thus contribute to the development of phytoremediation technologies for PCB-contaminated soils.

  8. Parasitoid complex of alfalfa aphids in an IPM intensive crop system in northern Catalonia

    Czech Academy of Sciences Publication Activity Database

    Pons, X.; Lumbierres, B.; Antoni, R.; Starý, Petr

    2011-01-01

    Roč. 84, č. 4 (2011), s. 437-445 ISSN 1612-4758 Grant - others:Universitat de Lleida(ES) CO8026; Universitat de Lleida(ES) CO9036 Institutional research plan: CEZ:AV0Z50070508 Keywords : alfalfa * Aphididae * Braconidae Subject RIV: EH - Ecology, Behaviour Impact factor: 1.509, year: 2011

  9. Uptake and translocation of sulfamethazine by alfalfa grown under hydroponic conditions.

    Science.gov (United States)

    Kurwadkar, Sudarshan; Struckhoff, Garrett; Pugh, Kameron; Singh, Om

    2017-03-01

    Antibiotics are routinely used in intensive animal agriculture operations collectively known as Concentrated Animal Feed Operations (CAFO) which include dairy, poultry and swine farms. Wastewater generated by CAFOs often contains low levels of antibiotics and is typically managed in an anaerobic lagoon. The objective of this research is to investigate the uptake and fate of aqueous sulfamethazine (SMN) antibiotic by alfalfa (Medicago sativa) grass grown under hydroponic conditions. Uptake studies were conducted using hydroponically grown alfalfa in a commercially available nutrient solution supplemented with 10mg/L of SMN antibiotic. Analysis of alfalfa sap, root zone, middle one-third, and top portion of the foliage showed varying uptake rate and translocation of SMN. The highest average amount of SMN (8.58μg/kg) was detected in the root zone, followed by the top portion (1.89μg/kg), middle one-third (1.30μg/kg), and sap (0.38μg/kg) samples, indicating a clear distribution of SMN within the sampled regions. The ultraviolet (UV) spectra of parent SMN and translocated SMN identified in different parts of the plant present the possibility of metabolization during the uptake process. Uptake of SMN using alfalfa grown under hydroponic conditions has potential as a promising remediation technology for removal of similar antibiotics from wastewater lagoons. Copyright © 2016. Published by Elsevier B.V.

  10. Chl1 DNA helicase regulates Scc2 deposition specifically during DNA-replication in Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Soumya Rudra

    Full Text Available The conserved family of cohesin proteins that mediate sister chromatid cohesion requires Scc2, Scc4 for chromatin-association and Eco1/Ctf7 for conversion to a tethering competent state. A popular model, based on the notion that cohesins form huge ring-like structures, is that Scc2, Scc4 function is essential only during G1 such that sister chromatid cohesion results simply from DNA replisome passage through pre-loaded cohesin rings. In such a scenario, cohesin deposition during G1 is temporally uncoupled from Eco1-dependent establishment reactions that occur during S-phase. Chl1 DNA helicase (homolog of human ChlR1/DDX11 and BACH1/BRIP1/FANCJ helicases implicated in Fanconi anemia, breast and ovarian cancer and Warsaw Breakage Syndrome plays a critical role in sister chromatid cohesion, however, the mechanism through which Chl1 promotes cohesion remains poorly understood. Here, we report that Chl1 promotes Scc2 loading unto DNA such that both Scc2 and cohesin enrichment to chromatin are defective in chl1 mutant cells. The results further show that both Chl1 expression and chromatin-recruitment are tightly regulated through the cell cycle, peaking during S-phase. Importantly, kinetic ChIP studies reveals that Chl1 is required for Scc2 chromatin-association specifically during S-phase, but not during G1. Despite normal chromatin enrichment of both Scc2 and cohesin during G1, chl1 mutant cells exhibit severe chromosome segregation and cohesion defects--revealing that G1-loaded cohesins is insufficient to promote cohesion. Based on these findings, we propose a new model wherein S-phase cohesin loading occurs during DNA replication and in concert with both cohesion establishment and chromatin assembly reactions--challenging the notion that DNA replication fork navigates through or around pre-loaded cohesin rings.

  11. Retinitis Pigmentosa Mutations in Bad Response to Refrigeration 2 (Brr2) Impair ATPase and Helicase Activity.

    Science.gov (United States)

    Ledoux, Sarah; Guthrie, Christine

    2016-06-03

    Brr2 is an RNA-dependent ATPase required to unwind the U4/U6 snRNA duplex during spliceosome assembly. Mutations within the ratchet helix of the Brr2 RNA binding channel result in a form of degenerative human blindness known as retinitis pigmentosa (RP). The biochemical consequences of these mutations on Brr2's RNA binding, helicase, and ATPase activity have not yet been characterized. Therefore, we identified the largest construct of Brr2 that is soluble in vitro, which truncates the first 247 amino acids of the N terminus (Δ247-Brr2), to characterize the effects of the RP mutations on Brr2 activity. The Δ247-Brr2 RP mutants exhibit a gradient of severity of weakened RNA binding, reduced helicase activity, and reduced ATPase activity compared with wild type Δ247-Brr2. The globular C-terminal Jab1/Mpn1-like domain of Prp8 increases the ability of Δ247-Brr2 to bind the U4/U6 snRNA duplex at high pH and increases Δ247-Brr2's RNA-dependent ATPase activity and the extent of RNA unwinding. However, this domain of Prp8 does not differentially affect the Δ247-Brr2 RP mutants compared with the wild type Δ247-Brr2. When stimulated by Prp8, wild type Δ247-Brr2 is able to unwind long stable duplexes in vitro, and even the RP mutants capable of binding RNA with tight affinity are incapable of fully unwinding short duplex RNAs. Our data suggest that the RP mutations within the ratchet helix impair Brr2 translocation through RNA helices. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. Putative neuroprotective agents in neuropsychiatric disorders.

    Science.gov (United States)

    Dodd, Seetal; Maes, Michael; Anderson, George; Dean, Olivia M; Moylan, Steven; Berk, Michael

    2013-04-05

    In many individuals with major neuropsychiatric disorders including depression, bipolar disorder and schizophrenia, their disease characteristics are consistent with a neuroprogressive illness. This includes progressive structural brain changes, cognitive and functional decline, poorer treatment response and an increasing vulnerability to relapse with chronicity. The underlying molecular mechanisms of neuroprogression are thought to include neurotrophins and regulation of neurogenesis and apoptosis, neurotransmitters, inflammatory, oxidative and nitrosative stress, mitochondrial dysfunction, cortisol and the hypothalamic-pituitary-adrenal axis, and epigenetic influences. Knowledge of the involvement of each of these pathways implies that specific agents that act on some or multiple of these pathways may thus block this cascade and have neuroprotective properties. This paper reviews the potential of the most promising of these agents, including lithium and other known psychotropics, aspirin, minocycline, statins, N-acetylcysteine, leptin and melatonin. These agents are putative neuroprotective agents for schizophrenia and mood disorders. Copyright © 2012 Elsevier Inc. All rights reserved.

  13. The Distributions of the Radionuclides Ra-226, Th-232 and K-40 in Various Parts of The Alfalfa Plant

    International Nuclear Information System (INIS)

    Salahel Din, K.; Harb, S.; Abbady, A.; Saad, N.

    2011-01-01

    The distribution of naturally occurring Ra-226, Th-232 and K-40 in different part of alfalfa plant from two different soils of Qena (South Valley University and Qena governorate farms) was studied under natural field conditions. Sixty two samples (alfalfa plant and its soil) were taken from nine sites inside farms. The samples were analyzed for their Ra-226, Th-232 and K-40 activity concentrations using gamma ray spectrometer consists of 3 x 3 NaI (Tl). The daily intakes of these radioisotopes by calves, milking cattle and sheep were calculated by multiplying concentrations in alfalfa and the daily consumption rates of these plants.

  14. [Natural nucleotide polymorphism of the Srlk gene that determines salt stress tolerance in alfalfa (Medicago sativa L)].

    Science.gov (United States)

    Vishnevskaia, M S; Pavlov, A V; Dziubenko, E A; Dziubenko, N I; Potokina, E K

    2014-04-01

    Based on legume genome syntheny, the nucleotide sequence of Srlk gene, key role of which in response to salt stress was demonstrated for the model species Medicago truncatula, was identified in the major forage and siderate crop alfalfa (Medicago sativa). In twelve alfalfa samples originating from regions with contrasting growing conditions, 19 SNPs were revealed in the Srlk gene. For two nonsynonymous SNPs, molecular markers were designed that could be further used to analyze the association between Srlk gene nucleotide polymorphism and the variability in salt stress tolerance among alfalfa cultivars.

  15. Effects of alfalfa germplasm and stage of maturity on digestive process and productive response of dairy cows fed alfalfa hay-based diets

    Directory of Open Access Journals (Sweden)

    Igino Andrighetto

    2010-01-01

    Full Text Available The effects on the digestive process and the productive performances of dairy cows fed diets containing alfalfa hay from  different germplasms and maturity were assessed in the present study. Three different lots of first-cut alfalfa hay were  used in the study: the improved variety “Boreal”, harvested at two consecutive maturity stages (early flowering and full  flowering and the ecotype “Vogherese”, at full flowering. Cutting the plant at an earlier stage of maturity improved hay  quality in comparison with the more mature forages (crude protein: 21.4 vs 16.5% DM; P  DM; P  er lignin content for the latter (8.6 vs 8.2% DM; P  tating cows were formulated using an equal amount of corn silage and the maximum inclusion of one of the tested hays  as forage base. The better quality of the early cut hay made it possible to increase its inclusion in the diet up to 44% of  total dietary DM, while the two more mature hays covered only 36% of total DM of the respective diets. According to a  3 x 3 Latin square design, the diets were fed to 3 Italian Brown cows (initial average days in milk 121 ± 24 and milk  yield 20 kg ± 1.3 fitted with ruminal cannula in 3 consecutive periods of 28 d each. Alfalfa stage of maturity and  germplasm did not affect dietary DM intake (average 16 kg/d. Degradability parameters of dietary DM, calculated by in  situ nylon bags technique, showed similar kinetics of rumen disappearance for all diets. No differences were noticed in  the ruminal rate of passage of the solid phase among diets, while the liquid phase showed a slower rate of passage for  the early flowering hay diet. Consistent with the degradation process, the stage of maturity or the alfalfa germplasm did  not affect the rumen fluid data or the in vivo digestibility coefficients of the diets. Milk yield did not show any change due  to either alfalfa maturity or cultivar, while milk protein was lowered when cows received the early cut hay

  16. Human regulator of telomere elongation helicase 1 (RTEL1) is required for the nuclear and cytoplasmic trafficking of pre-U2 RNA

    OpenAIRE

    Schertzer , Michael; Jouravleva , Karina; Perderiset , Mylène; Dingli , Florent; Loew , Damarys; Le Guen , Tangui; Bardoni , Barbara; De Villartay , Jean-Pierre; Revy , Patrick; Londono-Vallejo , Arturo

    2015-01-01

    International audience; Hoyeraal-Hreidarsson syndrome (HHS) is a severe form of Dyskeratosis congenita characterized by developmental defects, bone marrow failure and im-munodeficiency and has been associated with telom-ere dysfunction. Recently, mutations in Regulator of Telomere ELongation helicase 1 (RTEL1), a helicase first identified in Mus musculus as being responsible for the maintenance of long telomeres, have been identified in several HHS patients. Here we show that RTEL1 is require...

  17. Crop growth in early spring and radiation use efficiency in alfalfa

    International Nuclear Information System (INIS)

    Akmal, M.; Farid, U.; Asim, M.; Farhatullah, A.; Raziuddin, A.

    2011-01-01

    The study was conducted at Agronomy Research Farm, KP Agricultural University Peshawar. Fifteen alfalfa lines (M. sativa L.) were compared for crop growth rate (CGR), biomass yield and radiation use efficiency (RUE). The previous year experiment was defoliated on March, 13 2006 at ground levels about 5 cm height. Fertilizer to the crop was applied every year in first week of March to yield 30, 60, and 30 kg ha/sup -1/ N, P, and K, respectively after defoliation. Periodic samples were harvested from one meter row length at two locations and oven dried at 70 degree C for about 36 h. Before samples, periodic leaf area index (LAI) was recorded with LI-2000 (LI-COR, USA) and subsequently light measurements were made using data logger (LI-1400, LI-COR, USA) and light sensors LI-190 and LI-191 (LI-COR, USA). The CGR showed variation in shapes and asymptotes for the different alfalfa lines which resulted differences in both fresh and dry matters yield at final sampling harvest. Alfalfa line Gramma-2 was the highest in dry matter yield (110 g m-2) followed by Flewish-pop (107 g m-2). Alfalfa line Pumha with 74 g m-2 was the lowest in dry matter yield. Differences were observed in LAI (p<0.05). High dry matter yield of alfalfa line Gramma-2 was due to higher LAI which was associated to highest leaf fraction (38%). Differences in RUE were also observed among the lines. Flewish-pop was the highest in RUE (0.20 g DM MJ-2 PAR absorbed), followed by Gramma-2 (0.18 g DM MJ-2 PAR absorbed). Mean CGR and RUE of the different lines showed association with dry matter yield of which the lateral one showed a strong association compared with the earlier one. We conclude that higher RUE than CGR is important for the line/variety to get quality fodder production. (author)

  18. Effects of cold plasma treatment on alfalfa seed growth under simulated drought stress

    Science.gov (United States)

    Jinkui, FENG; Decheng, WANG; Changyong, SHAO; Lili, ZHANG; Xin, TANG

    2018-03-01

    The effect of different cold plasma treatments on the germination and seedling growth of alfalfa (Medicago sativa L.) seeds under simulated drought stress conditions was investigated. Polyethyleneglycol-6000 (PEG 6000)with the mass fraction of 0% (purified water), 5%, 10%, and 15% were applied to simulate the drought environment. The alfalfa seeds were treated with 15 different power levels ranged between 0-280 W for 15 s. The germination potential, germination rate, germination index, seedling root length, seedling height, and vigor index were investigated. Results indicated significant differences between treated with proper power and untreated alfalfa seeds. With the increase of treatment power, these indexes mentioned above almost presented bimodal curves. Under the different mass fractions of PEG 6000, results showed that the lower power led to increased germination, and the seedlings presented good adaptability to different drought conditions. Meanwhile, higher power levels resulted in a decreased germination rate. Seeds treated with 40 W resulted in higher germination potential, germination rate, seedling height, root length, and vigor index. Vigor indexes of the treated seeds under different PEG 6000 stresses increased by 38.68%, 43.91%, 74.34%, and 39.20% respectively compared to CK0-0, CK5-0, CK10-0, and CK15-0 (the control sample under 0%, 5%, 10%, and 15% PEG 6000). Therefore, 40 W was regarded as the best treatment in this research. Although the trend indexes of alfalfa seeds treated with the same power were statistically the same under different PEG 6000 stresses, the cold plasma treatment had a significant effect on the adaptability of alfalfa seeds in different drought environments. Thus, this kind of treatment is worth implementing to promote seed growth under drought situations.

  19. The impact of lignin downregulation on alfalfa yield, chemical composition, and in vitro gas production.

    Science.gov (United States)

    Getachew, Girma; Laca, Emilio A; Putnam, Daniel H; Witte, Dave; McCaslin, Mark; Ortega, Kara P; DePeters, Edward J

    2018-02-06

    Lignin is a complex, phenolic polymer found in plant cell walls that is essential for mechanical support, water and mineral transport, and defense in vascular plants. Over ten different enzymes play a role in the synthesis of lignin in plants. Suppression of any one enzyme or combinations of these enzymes may change the concentration and composition of lignin in the genetically transformed plants. Two lines of alfalfa that were downregulated for caffeoyl coenzyme A O-methyltransferase were used to assess the impact of lignin downregulation on chemical composition and fermentation rate and extent using an in vitro gas production technique. A total of 64 samples consisting of two reduced lignin (RL) and two controls (CL), four field replicates, two cutting intervals (CIs; 28 and 35 days), and two cuts (Cut-1 and Cut-3) were used. No differences were detected in yield, crude protein, neutral detergent fiber (aNDF), and acid detergent fiber between the lines when harvested at the 28-day CI. The acid detergent lignin (ADL) concentration in RL alfalfa lines was significantly (P gas production and metabolizable energy content were greater in RL than in CL alfalfa. RL lines had 3.8% indigestible aNDF per unit ADL, whereas CL had 3.4% (P < 0.01). The positive effect of lignin downregulation was more pronounced when intervals between harvests were longer (35-day CI compared with the 28-day CI). Lignin downregulation in alfalfa offers an opportunity to extend harvesting time (CI) for higher yield without compromising the nutritional quality of the alfalfa forage for dairy and livestock feeding. However, the in vitro results reported here warrant further study using in vivo methods. © 2018 Society of Chemical Industry. © 2018 Society of Chemical Industry.

  20. Identification and Biochemical Characterization of Halisulfate 3 and Suvanine as Novel Inhibitors of Hepatitis C Virus NS3 Helicase from a Marine Sponge

    Directory of Open Access Journals (Sweden)

    Atsushi Furuta

    2014-01-01

    Full Text Available Hepatitis C virus (HCV is an important etiological agent that is responsible for the development of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. HCV nonstructural protein 3 (NS3 helicase is a possible target for novel drug development due to its essential role in viral replication. In this study, we identified halisulfate 3 (hal3 and suvanine as novel NS3 helicase inhibitors, with IC50 values of 4 and 3 µM, respectively, from a marine sponge by screening extracts of marine organisms. Both hal3 and suvanine inhibited the ATPase, RNA binding, and serine protease activities of NS3 helicase with IC50 values of 8, 8, and 14 µM, and 7, 3, and 34 µM, respectively. However, the dengue virus (DENV NS3 helicase, which shares a catalytic core (consisting mainly of ATPase and RNA binding sites with HCV NS3 helicase, was not inhibited by hal3 and suvanine, even at concentrations of 100 µM. Therefore, we conclude that hal3 and suvanine specifically inhibit HCV NS3 helicase via an interaction with an allosteric site in NS3 rather than binding to the catalytic core. This led to the inhibition of all NS3 activities, presumably by inducing conformational changes.

  1. Crystal structure of isoflavone reductase from alfalfa (Medicago sativa L.).

    Science.gov (United States)

    Wang, Xiaoqiang; He, Xianzhi; Lin, Jianqiao; Shao, Hui; Chang, Zhenzhan; Dixon, Richard A

    2006-05-19

    Isoflavonoids play important roles in plant defense and exhibit a range of mammalian health-promoting activities. Isoflavone reductase (IFR) specifically recognizes isoflavones and catalyzes a stereospecific NADPH-dependent reduction to (3R)-isoflavanone. The crystal structure of Medicago sativa IFR with deletion of residues 39-47 has been determined at 1.6A resolution. Structural analysis, molecular modeling and docking, and comparison with the structures of other NADPH-dependent enzymes, defined the putative binding sites for co-factor and substrate and potential key residues for enzyme activity and substrate specificity. Further mutagenesis has confirmed the role of Lys144 as a catalytic residue. This study provides a structural basis for understanding the enzymatic mechanism and substrate specificity of IFRs as well as the functions of IFR-like proteins.

  2. Analysis of Hydraulic Flood Control Structure at Putat Boro River

    OpenAIRE

    Ruzziyatno, Ruhban

    2015-01-01

    Putat Boro River is one of the main drainage systems of Surakarta city which drains into Bengawan Solo river. The primary problem when flood occur is the higher water level of Bengawan Solo than Boro River and then backwater occur and inundates Putat Boro River. The objective of the study is to obtain operational method of Putat Boro River floodgate to control both inflows and outflows not only during flood but also normal condition. It also aims to know the Putat Boro rivers floodgate op...

  3. Environmental life cycle assessment of producing willow, alfalfa and straw from spring barley as feedstocks for bioenergy or biorefinery systems

    DEFF Research Database (Denmark)

    Parajuli, Ranjan; Knudsen, Marie Trydeman; Djomo, Sylvestre Njakou

    2017-01-01

    The current study aimed at evaluating potential environmental impacts for the production of willow, alfalfa and straw from spring barley as feedstocks for bioenergy or biorefinery systems. A method of Life Cycle Assessment was used to evaluate based on the following impact categories: Global...... and land occupation. Environmental impacts for straw were economically allocated from the impacts obtained for spring barley. The results obtained per ton dry matter showed a lower carbon footprint for willow and alfalfa compared to straw. It was due to higher soil carbon sequestration and lower N2O...... emissions. Likewise, willow and alfalfa had lower EP than straw. Straw had lowest NRE use compared to other biomasses. PFWTox was lower in willow and alfalfa compared to straw. A critical negative effect on soil quality was found with the spring barley production and hence for straw. Based on the energy...

  4. The DEAD-Box RNA Helicase DDX3 Interacts with m6A RNA Demethylase ALKBH5

    Directory of Open Access Journals (Sweden)

    Abdullah Shah

    2017-01-01

    Full Text Available DDX3 is a member of the family of DEAD-box RNA helicases. DDX3 is a multifaceted helicase and plays essential roles in key biological processes such as cell cycle, stress response, apoptosis, and RNA metabolism. In this study, we found that DDX3 interacted with ALKBH5, an m6A RNA demethylase. The ATP domain of DDX3 and DSBH domain of ALKBH5 were indispensable to their interaction with each other. Furthermore, DDX3 could modulate the demethylation of mRNAs. We also showed that DDX3 regulated the methylation status of microRNAs and there was an interaction between DDX3 and AGO2. The dynamics of m6A RNA modification is still a field demanding further investigation, and here, we add a link by showing that RNA demethylation can be regulated by proteins such as DDX3.

  5. Mutations of the RTEL1 Helicase in a Hoyeraal-Hreidarsson Syndrome Patient Highlight the Importance of the ARCH Domain.

    Science.gov (United States)

    Jullien, Laurent; Kannengiesser, Caroline; Kermasson, Laetitia; Cormier-Daire, Valérie; Leblanc, Thierry; Soulier, Jean; Londono-Vallejo, Arturo; de Villartay, Jean-Pierre; Callebaut, Isabelle; Revy, Patrick

    2016-05-01

    The DNA helicase RTEL1 participates in telomere maintenance and genome stability. Biallelic mutations in the RTEL1 gene account for the severe telomere biology disorder characteristic of the Hoyeraal-Hreidarsson syndrome (HH). Here, we report a HH patient (P4) carrying two novel compound heterozygous mutations in RTEL1: a premature stop codon (c.949A>T, p.Lys317*) and an intronic deletion leading to an exon skipping and an in-frame deletion of 25 amino-acids (p.Ile398_Lys422). P4's cells exhibit short and dysfunctional telomeres similarly to other RTEL1-deficient patients. 3D structure predictions indicated that the p.Ile398_Lys422 deletion affects a part of the helicase ARCH domain, which lines the pore formed with the core HD and the iron-sulfur cluster domains and is highly specific of sequences from the eukaryotic XPD family members. © 2016 WILEY PERIODICALS, INC.

  6. Essential and distinct roles of the F-box and helicase domains of Fbh1 in DNA damage repair

    Directory of Open Access Journals (Sweden)

    Shinagawa Hideo

    2008-03-01

    Full Text Available Abstract Background DNA double-strand breaks (DSBs are induced by exogenous insults such as ionizing radiation and chemical exposure, and they can also arise as a consequence of stalled or collapsed DNA replication forks. Failure to repair DSBs can lead to genomic instability or cell death and cancer in higher eukaryotes. The Schizosaccharomyces pombe fbh1 gene encodes an F-box DNA helicase previously described to play a role in the Rhp51 (an orthologue of S. cerevisiae RAD51-dependent recombinational repair of DSBs. Fbh1 fused to GFP localizes to discrete nuclear foci following DNA damage. Results To determine the functional roles of the highly conserved F-box and helicase domains, we have characterized fbh1 mutants carrying specific mutations in these domains. We show that the F-box mutation fbh1-fb disturbs the nuclear localization of Fbh1, conferring an fbh1 null-like phenotype. Moreover, nuclear foci do not form in fbh1-fb cells with DNA damage even if Fbh1-fb is targeted to the nucleus by fusion to a nuclear localization signal sequence. In contrast, the helicase mutation fbh1-hl causes the accumulation of Fbh1 foci irrespective of the presence of DNA damage and confers damage sensitivity greater than that conferred by the null allele. Additional mutation of the F-box alleviates the hypermorphic phenotype of the fbh1-hl mutant. Conclusion These results suggest that the F-box and DNA helicase domains play indispensable but distinct roles in Fbh1 function. Assembly of the SCFFbh1 complex is required for both the nuclear localization and DNA damage-induced focus formation of Fbh1 and is therefore prerequisite for the Fbh1 recombination function.

  7. DEAD-Box RNA Helicases are among the Constituents of the Tobacco Pollen mRNA Storing Bodies

    Czech Academy of Sciences Publication Activity Database

    Hafidh, Said; Potěšil, D.; Zdráhal, Z.; Honys, David

    2013-01-01

    Roč. 1, č. 3 (2013) ISSN 2329-9029 R&D Projects: GA ČR GPP501/11/P321; GA ČR(CZ) GAP501/11/1462; GA MŠk(CZ) ED1.1.00/02.0068; GA MŠk(CZ) LD13049 Institutional support: RVO:61389030 Keywords : Translation * mRNA storage * RNA helicase Subject RIV: EB - Genetics ; Molecular Biology

  8. JST Thesaurus Headwords and Synonyms: alfalfa mosaic virus [MeCab user dictionary for science technology term[Archive

    Lifescience Database Archive (English)

    Full Text Available MeCab user dictionary for science technology term alfalfa mosaic virus 名詞 一般 * * * * アルファルファモザイクウイルス アルファルファ...モザイクウイルス アルファルファモザイクーイルス Thesaurus2015 200906086556609347 C LS07 UNKNOWN_2 alfalfa mosaic virus

  9. Putative bronchopulmonary flagellated protozoa in immunosuppressed patients.

    Science.gov (United States)

    Kilimcioglu, Ali Ahmet; Havlucu, Yavuz; Girginkardesler, Nogay; Celik, Pınar; Yereli, Kor; Özbilgin, Ahmet

    2014-01-01

    Flagellated protozoa that cause bronchopulmonary symptoms in humans are commonly neglected. These protozoal forms which were presumed to be "flagellated protozoa" have been previously identified in immunosuppressed patients in a number of studies, but have not been certainly classified so far. Since no human cases of bronchopulmonary flagellated protozoa were reported from Turkey, we aimed to investigate these putative protozoa in immunosuppressed patients who are particularly at risk of infectious diseases. Bronchoalveolar lavage fluid samples of 110 immunosuppressed adult patients who were admitted to the Department of Chest Diseases, Hafsa Sultan Hospital of Celal Bayar University, Manisa, Turkey, were examined in terms of parasites by light microscopy. Flagellated protozoal forms were detected in nine (8.2%) of 110 cases. Metronidazole (500 mg b.i.d. for 30 days) was given to all positive cases and a second bronchoscopy was performed at the end of the treatment, which revealed no parasites. In conclusion, immunosuppressed patients with bronchopulmonary symptoms should attentively be examined with regard to flagellated protozoa which can easily be misidentified as epithelial cells.

  10. Toddlers’ Duration of Attention towards Putative Threat

    Science.gov (United States)

    Kiel, Elizabeth J.; Buss, Kristin A.

    2010-01-01

    Although individual differences in reactions to novelty in the toddler years have been consistently linked to risk for developing anxious behavior, toddlers’ attention towards a novel, putatively threatening stimulus while in the presence of other enjoyable activities has rarely been examined as a precursor to such risk. The current study examined how attention towards an angry-looking gorilla mask in a room with alternative opportunities for play in 24-month-old toddlers predicted social inhibition when children entered kindergarten. Analyses examined attention to threat above and beyond and in interaction with both proximity to the mask and fear of novelty observed in other situations. Attention to threat interacted with proximity to the mask to predict social inhibition, such that attention to threat most strongly predicted social inhibition when toddlers stayed furthest from the mask. This relation occurred above and beyond the predictive relation between fear of novelty and social inhibition. Results are discussed within the broader literature of anxiety development and attentional processes in young children. PMID:21373365

  11. Effect of Arbuscular Mycorrhizal Fungi Glomus spp. Inoculation on Alfalfa Growth in Soils with Copper Efecto de la Inoculación con Hongos Micorrízicos Arbusculares Glomus spp. sobre el Crecimiento de Alfalfa en Suelos con Cobre

    Directory of Open Access Journals (Sweden)

    Daniela Novoa M

    2010-06-01

    Full Text Available Soils near mining centers usually have high heavy metal (HM levels. It has been found that some plants associated with arbuscular mycorrhizal fungi (AMF improve growth and tolerance to HM in soils. This symbiosis is a biological resource for degraded soil recovery. The objective of this study was to determine the effect of inoculating AMF (Glomus spp. on alfalfa (Medicago sativa L. growth in agricultural soils with different copper (Cu levels for degraded soil recovery. To this effect, alfalfa seeds were grown in soils from the Catemu and Casablanca valleys and inoculated with AMF. Plant height, stem diameter, and number of leaves were measured weekly. Dry matter, mycorrhizal colonization, and Cu concentration in alfalfa plant tissues were measured after 81 days. Inoculation increased plant height by 24%, stem diameter by 11%, and number of leaves by 34%. Inoculation had a significant effect (p ≤ 0.05 on alfalfa plants that were grown in soil with the highest Cu concentration, but had no effect on Cu accumulation in alfalfa plant tissues. A direct relationship was observed between Cu accumulation in alfalfa and Cu concentration in soils. It was concluded that alfalfa inoculated with Glomus spp. is applicable to the soil recovery process whenever soil properties can ensure inoculum effectiveness on alfalfa growth, and avoid toxicity by excessive Cu in alfalfa plant tissues.Los suelos cercanos a centros de actividad minera suelen presentar altos niveles de metales pesados (HM. Se ha encontrado que algunas plantas asociadas a hongos micorrízicos arbusculares (AMF mejoran su crecimiento y tolerancia a los HM presentes en los suelos. Esta simbiosis constituye un recurso biológico para la recuperación de suelos degradados. El objetivo de este estudio fue determinar el efecto de la inoculación con AMF (Glomus spp. sobre el crecimiento de alfalfa (Medicago sativa L. en suelos agrícolas con distintos niveles de cobre (Cu para la recuperación de

  12. Structural Studies of RNA Helicases Involved in Eukaryotic Pre-mRNA Splicing, Ribosome Biogenesis, and Translation Initiation

    DEFF Research Database (Denmark)

    He, Yangzi

    and ligates the neighbouring exons to generate mature mRNAs. Prp43 is an RNA helicase of the DEAH/RHA family. In yeast, once mRNAs are released, Prp43 catalyzes the disassembly of spliceosomes. The 18S, 5.8S and 25S rRNAs are transcribed as a single polycistronic transcript—the 35S pre......-rRNA. It is nucleolytically cleaved and chemically modified to generate mature rRNAs, which assemble with ribosomal proteins to form the ribosome. Prp43 is required for the processing of the 18S rRNA. Using X-ray crystallography, I determined a high resolution structure of Prp43 bound to ADP, the first structure of a DEAH....../RHA helicase. It defined the conserved structural features of all DEAH/RHA helicases, and unveiled a novel nucleotide binding site. Additionally a preliminary low resolution structure of a ternary complex comprising Prp43, a non-hydrolyzable ATP analogue, and a single-stranded RNA, was obtained. The ribosome...

  13. Zebrafish P54 RNA helicases are cytoplasmic granule residents that are required for development and stress resilience

    Directory of Open Access Journals (Sweden)

    Cecilia Zampedri

    2016-10-01

    Full Text Available Stress granules are cytoplasmic foci that directly respond to the protein synthesis status of the cell. Various environmental insults, such as oxidative stress or extreme heat, block protein synthesis; consequently, mRNA will stall in translation, and stress granules will immediately form and become enriched with mRNAs. P54 DEAD box RNA helicases are components of RNA granules such as P-bodies and stress granules. We studied the expression, in cytoplasmic foci, of both zebrafish P54 RNA helicases (P54a and P54b during development and found that they are expressed in cytoplasmic granules under both normal conditions and stress conditions. In zebrafish embryos exposed to heat shock, some proportion of P54a and P54b helicases move to larger granules that exhibit the properties of genuine stress granules. Knockdown of P54a and/or P54b in zebrafish embryos produces developmental abnormalities restricted to the posterior trunk; further, these embryos do not form stress granules, and their survival upon exposure to heat-shock conditions is compromised. Our observations fit the model that cells lacking stress granules have no resilience or ability to recover once the stress has ended, indicating that stress granules play an essential role in the way organisms adapt to a changing environment.

  14. Impact of field dodder (Cuscuta campestris Yunk. on physiological and anatomical changes in untreated and herbicide-treated alfalfa plants

    Directory of Open Access Journals (Sweden)

    Sarić-Krsmanović Marija

    2016-01-01

    Full Text Available The effects of field dodder on physiological processes and the anatomy of alfalfa plants were examined under controlled conditions. The experiment included the following variants: N - noninfested alfalfa plants (control; I - infested alfalfa plants (untreated; T - infested plants treated with imazethapyr. Imazethapyr application rate was 100 g a.i. ha-1. The following parameters were checked: physiological - pigment content (chlorophyll ɑ, chlorophyll b, total carotenoids; anatomical - stem parameters: thickness of epidermis and cortex, and diameter of stem and central cylinder; leaf parameters: thickness of epidermis, parenchyma and spongy tissue, mesophyll and underside leaf epidermis, and diameter of bundle sheath cells in alfalfa plants. Pigment contents and anatomical parameters were measured: prior to herbicide treatment (0 assessment, then 7 (I assessment, 14 (II assessment, 21 (III assessment, 28 (IV assessment and 35 (V assessment days after application (DAA. Field dodder was found to affect the contents of chlorophyll ɑ, chlorophyll ɑ and carotenoids in untreated alfalfa plants, causing significant reductions in pigment content. Conversely, percent reduction in the treated plants decreased 22-5% for chlorophyll ɑ, 25-1%, for chlorophyll b, and 21-11% for carotenoids, while a stimulating effect of 1-6% was observed for the contents of chlorophyll b and carotenoids 35 DAA. Plants infested (untreated by field dodder had lower values of most anatomical parameters, compared to noninfested plants. The measured anatomical parameters of alfalfa stems and leaves had significantly higher values in noninfested plants and plants treated with imazethapyr than in untreated plants.

  15. Alfalfa nutritive quality for ruminant livestock as influenced by ambient air quality in west-central Alberta

    International Nuclear Information System (INIS)

    Lin, J.C.; Nosal, M.; Muntifering, R.B.; Krupa, S.V.

    2007-01-01

    Alfalfa (Medicago sativa) nutritive quality response to ambient ozone (O 3 ), sulfur dioxide (SO 2 ) and oxides of nitrogen (NO x ) were assessed at three locations in west-central Alberta, Canada (1998-2002). Yield data were segregated into high and low relative to overall median yield. Ozone concentrations (hourly median and 95th-percentile) and precipitation (P) contributed 69 and 29%, respectively, to the variability in crude protein (CP) concentration in low-yielding alfalfa, whereas mean temperature (T) and relative humidity (RH) collectively influenced 98% of the variation in CP in high-yielding alfalfa. Three-fourths of the accounted variation in relative feed value (RFV) of low-yielding alfalfa was attributable to P, T and RH, whereas median and 95th-percentile hourly O 3 concentrations and SO 2 and NO x exposure integrals contributed 25%. In contrast, air quality, (mainly O 3 ) influenced 86% of the accounted variation in RFV of high-yielding alfalfa, and T and P collectively contributed 14%. - Exposure to ambient concentrations of phytotoxic air pollutants affected nutritive quality of alfalfa for ruminant livestock in a yield-dependent manner

  16. Alfalfa nutritive quality for ruminant livestock as influenced by ambient air quality in west-central Alberta

    Energy Technology Data Exchange (ETDEWEB)

    Lin, J.C. [Department of Animal Sciences, Auburn University, Auburn, AL 36849 (United States); Nosal, M. [Department of Mathematics and Statistics, University of Calgary, Calgary, AB T2N 1N4 (Canada); Muntifering, R.B. [Department of Animal Sciences, Auburn University, Auburn, AL 36849 (United States)]. E-mail: muntirb@auburn.edu; Krupa, S.V. [Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108 (United States)

    2007-09-15

    Alfalfa (Medicago sativa) nutritive quality response to ambient ozone (O{sub 3}), sulfur dioxide (SO{sub 2}) and oxides of nitrogen (NO {sub x} ) were assessed at three locations in west-central Alberta, Canada (1998-2002). Yield data were segregated into high and low relative to overall median yield. Ozone concentrations (hourly median and 95th-percentile) and precipitation (P) contributed 69 and 29%, respectively, to the variability in crude protein (CP) concentration in low-yielding alfalfa, whereas mean temperature (T) and relative humidity (RH) collectively influenced 98% of the variation in CP in high-yielding alfalfa. Three-fourths of the accounted variation in relative feed value (RFV) of low-yielding alfalfa was attributable to P, T and RH, whereas median and 95th-percentile hourly O{sub 3} concentrations and SO{sub 2} and NO {sub x} exposure integrals contributed 25%. In contrast, air quality, (mainly O{sub 3}) influenced 86% of the accounted variation in RFV of high-yielding alfalfa, and T and P collectively contributed 14%. - Exposure to ambient concentrations of phytotoxic air pollutants affected nutritive quality of alfalfa for ruminant livestock in a yield-dependent manner.

  17. Preliminary Study on Effect of Herbicides on Alfalfa Yield and Weed Community Characteristics in Yellow River Delta, China

    Directory of Open Access Journals (Sweden)

    WANG Guo-liang

    2016-05-01

    Full Text Available Alfalfa(Medicago sativa is one of important legume forages worldwide. However, weed is the main factor limiting alfalfa production. Biomass quality and yield and stability of dry matter production during cultivation are directly associated with the interference of weeds which compete with alfalfa for water, light and nutrients. The use of herbicides is a good alternative for weed control. In order to control weed in alfalfa field with suitable herbicide in Yellow River delta, the effect of four herbicides(imazethapyr, quizalofop-p-ethyl, haloxyfop-r-methyl and oxyfluorfen with different concentration on afalfal yield and weed community characteristics were studied. The results showed that both imazethapyr and haloxyfop-r-methyl treatments could increase alfalfa yield, and the best herbicide application concentration was imazethapyr with 2 000 mL·hm-2 and haloxyfop-r-methyl with 700 mL·hm-2, but oxyfluorfen treatment would limit alfalfa growth significantly. Weed species numbers in the treatments of imazethapyr, quizalofop-p-ethyl and oxyfluorfen decreased significantly. Digitariasanguinalis, Portulacaoleracea and Echinochloacrusgalli were more difficult to control from specie important value in all treatments. Species diversity index decreased with higher herbicide concentration in all treatments. From this study, herbicide imazethapyr with 2 000 mL·hm-2 application concentration was the best weed control method, and the second one was haloxyfop-r-methyl with 700 mL·hm-2 application concentration.

  18. Contrasting Strategies of Alfalfa Stem Elongation in Response to Fall Dormancy in Early Growth Stage: The Tradeoff between Internode Length and Internode Number

    Science.gov (United States)

    Wang, Zongli; Sun, Qizhong

    2015-01-01

    Fall dormancy (FD) in alfalfa (Medicago sativa L.) can be described using 11 FD ratings, is widely used as an important indicator of stress resistance, productive performance and spring growth. However, the contrasting growth strategies in internode length and internode number in alfalfa cultivars with different FD rating are poorly understood. Here, a growth chamber study was conducted to investigate the effect of FD on plant height, aboveground biomass, internode length, and internode number in alfalfa individuals in the early growth stages. In order to simulate the alfalfa growth environment in the early stage, 11 alfalfa cultivars with FD ratings from one to 11 were chosen and seeded at the greenhouse, and then were transplanted into an artificial growth chamber. The experimental design was a randomized complete block in a split-plot arrangement with three replicates. Plant height, above-ground biomass, internode length, and internode number were measured in early growth stage in all individuals. Our findings showed that plant height and the aboveground biomass of alfalfa did not significantly differ among 11 different FD rated cultivars. Also, internode length and internode number positively affected plant height and the aboveground biomass of alfalfa individuals and the average internode length significantly increased with increasing FD rating. However, internode number tended to sharply decline when the FD rating increased. Moreover, there were no correlations, slightly negative correlations, and strongly negative correlations between internode length and internode number in alfalfa individuals among the three scales, including within-FD ratings, within-FD categories and inter-FD ratings, respectively. Therefore, our results highlighted that contrasting growth strategies in stem elongation were adopted by alfalfa with different FD ratings in the early growth stage. Alfalfa cultivars with a high FD rating have longer internodes, whereas more dormant alfalfa

  19. Twenty putative palmitoyl-acyl transferase genes with distinct ...

    African Journals Online (AJOL)

    There are 20 genes containing DHHC domain predicted to encode putative palmitoyltransferase in Arabidopsis thaliana genome. However, little is known about their characteristics such as genetic relationship and expression profile. Here, we present an overview of the putative PAT genes in A. thaliana focusing on their ...

  20. Putative radioresistant bacterial isolate from sewage water

    International Nuclear Information System (INIS)

    Ang, April; Chua, Patricia; Perez, Kristine; Rey, April; Rivor Kristel; San Pablo, Czarina; Santos, Ernestine

    2001-01-01

    Sewage water was collected from a stagnant body of water in Balara, Quezon City. approximately 150 ml was aseptically transferred into eight Erlenmeyer flasks. Seven flasks were then subjected to different doses of radiation at the 60 Co irradiation facility, PNRI (Philippine Nuclear Research Institute) which are as follows: 0.01 kGy, 0.1 kGy, 0.5 kGy, 1 kGy, 5 kGy, 10 kGy, and 15 kGy. The remaining flask was used as the control. After irradiation, all the different treatments were subjected to colony count at the culture collection laboratory, NSRI. Results showed that the colonies from sewage water treatments irradiated at 0.01 kGy (treatment A), 0.10 kGy (treatment B), and 0.50 kGy (treatment C) exhibited a decreasing trend with colony counts 4.60 x 10 3 CFU/ml, and 1.30 x 10 3 CFU/ml, and 26 CFU/ml, respectively. Contrastingly, at 1 kGy (treatment D), high colony count of 2.95 x 10 3 CFU/ml was observed which is even higher compared to the control (1.02 x 10 3 CFU/ml). Treatment E that was irradiated at 5 kGy manifested low survival rate (25 CFU/ml) indicating the presence of few putative intermediate radioresistant bacteria. Radiation dose treatments higher than 5 kGy (i.e., 10 kGy and 15 kGy) exhibited no bacterial survival. (Author)

  1. Putative radioresistant bacterial isolate from sewage water

    Energy Technology Data Exchange (ETDEWEB)

    Ang, April; Chua, Patricia; Perez, Kristine; Rey, April; Kristel, Rivor; San Pablo, Czarina; Santos, Ernestine

    2001-01-29

    Sewage water was collected from a stagnant body of water in Balara, Quezon City. approximately 150 ml was aseptically transferred into eight Erlenmeyer flasks. Seven flasks were then subjected to different doses of radiation at the {sup 60}Co irradiation facility, PNRI (Philippine Nuclear Research Institute) which are as follows: 0.01 kGy, 0.1 kGy, 0.5 kGy, 1 kGy, 5 kGy, 10 kGy, and 15 kGy. The remaining flask was used as the control. After irradiation, all the different treatments were subjected to colony count at the culture collection laboratory, NSRI. Results showed that the colonies from sewage water treatments irradiated at 0.01 kGy (treatment A), 0.10 kGy (treatment B), and 0.50 kGy (treatment C) exhibited a decreasing trend with colony counts 4.60 x 10{sup 3} CFU/ml, and 1.30 x 10{sup 3} CFU/ml, and 26 CFU/ml, respectively. Contrastingly, at 1 kGy (treatment D), high colony count of 2.95 x 10{sup 3} CFU/ml was observed which is even higher compared to the control (1.02 x 10{sup 3} CFU/ml). Treatment E that was irradiated at 5 kGy manifested low survival rate (25 CFU/ml) indicating the presence of few putative intermediate radioresistant bacteria. Radiation dose treatments higher than 5 kGy (i.e., 10 kGy and 15 kGy) exhibited no bacterial survival. (Author)

  2. Resistance and susceptibility of alfalfa (Medicago sativa L.) cultivars to the aphid Therioaphis maculata (Homoptera:Aphididae): insect biology and cultivar evaluation

    Institute of Scientific and Technical Information of China (English)

    ALEXANDRE DE ALMEIDA E SILVA; ELENICE MOURO VARANDA; JOS(E) RICARDO BAROSELA

    2006-01-01

    Biology of the aphid Therioaphis maculata was studied on alfalfa (Medicago sativa L.), including four resistant (Mesa-Sirsa, CUF101, Baker and Lahontan) and two susceptible (ARC and Caliverde) alfalfa cultivars, and one of the most cropped Brazilian cultivars, Crioula. Under controlled conditions, antibiosis (i.e., reduced longevity, fecundity and increased mortality of the aphid) was observed mainly on the resistant alfalfa cultivars,except on Lahontan. Crioula seemed to be tolerant to aphids. Present data support geographic limitation usage of cultivars, and we suggest Baker and Mesa-Sirsa as sources of antibiosis,and provide biological information of a tropical T. maculata biotype on alfalfa.

  3. Effects of enhanced UVB on growth and yield of alfalfa and soybean under field conditions

    International Nuclear Information System (INIS)

    Al-Oudat, M.; Baydon, S.A.; Mohamad, A.

    1998-01-01

    The effects of 20% increase of UVB on growth and yield of alfalfa (Medicago Sativa L.) and two cultivars of soybean (Glycine Max (L.) Mer) under field conditions have been investigated. The increase of UVB dose ranged between 1.746 and 7.112 J/cm 2 during experiment. The results showed that soybean yield decrease by 16% and 31% in A. 3803 and A. 2522 cultivars respectively, under UVB exposure. The dry weight and leaf area were sensitive in the A. 3803 cultivar, while they were tolerant in the A. 2522 cultivar. Alfalfa response to UVB varied during the different stages of growth, whereas the yield was 12% less in the exposed plants. (author)

  4. Digital gene-expression of alfalfa saponin extract on laying hens

    Directory of Open Access Journals (Sweden)

    Wenna Fan

    2015-03-01

    Full Text Available Cardiovascular disease is a major cause of death worldwide, so people are advised to limit their intake of dietary cholesterol [1]. Egg consumption has been seriously reduced because of the high levels of cholesterol [2]. The objective of this study was to evaluate the cholesterol metabolism effects of alfalfa saponin extract (ASE in liver and ovary tissues using digital gene-expression (DGE profiling analysis. The liver and ovary tissues were isolated from laying hens fed with ASE for RNA sequencing. Here, we provide detailed experimental methods and analysis pipeline in our study to identify digital gene expression of alfalfa saponin extract on laying hens and analysis pipeline published by Singh and colleagues in the PLOS ONE [3]. The data generated in our work provide meaningful information for understanding the molecular mechanisms underlying the cholesterol-lowering effects of ASE.

  5. Phytoremediation of polycyclic aromatic hydrocarbons (PAH) by cv. Crioula: A Brazilian alfalfa cultivar.

    Science.gov (United States)

    Alves, Wilber S; Manoel, Evelin A; Santos, Noemi S; Nunes, Rosane O; Domiciano, Giselli C; Soares, Marcia R

    2018-07-03

    This work aimed to evaluate the phytoremediation capacity of the alfalfa cultivar Crioula in soils contaminated with polycyclic aromatic hydrocarbons (PAHs), primary pollutants with mutagenic and carcinogenic potential. Alfalfa was grown from seed for 40 days on soil amended with anthracene, pyrene, and phenanthrene. Soil and plant tissue was collected for biometric assay, dry mass analysis, and PAH analysis by liquid chromatography. Increased total PAH concentration was associated with decreases in plant biomass, height, and internode length. The Crioula cultivar had a satisfactory phytoremediation effect, reducing total PAH concentration (300 ppm) in the experimental soil by 85% in 20 days, and by more than 95% in 40 days. The PAH showed a tendency to be removed in the temporal order: phenanthrene before pyrene before anthracene, and the removal ratio was influenced by the initial soil concentration of each PAH.

  6. Reaction of the Lithuanian alfalfa breeding populations to Phoma medicaginis under cool temperate climate conditions

    International Nuclear Information System (INIS)

    Liatukiene, A.; Liatukas, Z.; Ruzgas, V.

    2015-01-01

    The alfalfa Phoma medicaginis resistance was evaluated on 100 accessions with different development date. Weather conditions favoured high disease pressure and differentiation of tested accessions was not clear in 2011. Accessions were compared by maximal disease severity (DS) and area under disease progress curve (AUDPC). DS ranged from 10 to 60% and AUDPC value ranged 119-727 in 2009. DS and AUDPC values were higher in 2010 and 2011, DS ranged 40-65 and 66-68% and AUDPC ranged 2263-2928 and 2853-3006. Development date of accessions showed low impact on resistance. The correlations between DS and AUDPC results of accessions across years highly varied (r=0.189 - 0.828) due to low differentiation of accessions resistance. Selection of alfalfa material promising by Phoma medicaginis resistance should be done under conditions moderately favourable for development of this disease. (author)

  7. Cytological changes of root tip cells of alfalfa seeds after space flight

    International Nuclear Information System (INIS)

    Ren Weibo; Xu Zhu; Chen Libo; Guo Huiqin; Wang Mi; Zhao Liang

    2008-01-01

    To understand the cytological effects of space flight on alfalfa seeds, dry seeds of three lines (Line 1, Line 2 and Line 4) were selected and loaded onto 'Shijian No.8' satellite for space flight. After returning to the ground, root tips of alfalfa were clipped and chromosome aberrations were observed by microscope. Data showed that space flight had two types of effect on cell mitotic: one was positive (Line 2, Line 4) and the other was negative (Line 1). Such chromosome aberrations were observed as micronucleus, chromosome bridge, fragments, lagging and so on. The frequency of aberration varied with the different materials. Conclusion was that space flight had significant effect on root tip cells, which mainly showed as the chromosome aberrations. (authors)

  8. Population Dynamics of Empoasca fabae (Hemiptera: Cicadellidae) in Central Iowa Alfalfa Fields

    Science.gov (United States)

    Weiser Erlandson, L. A.; Obrycki, J. J.

    2015-01-01

    Adults and nymphs of Empoasca fabae Harris (Hemiptera: Cicadellidae) and adults of predatory species in the families Coccinellidae, Anthocoridae, Nabidae, Chrysopidae, and Hemerobiidae were sampled in Iowa alfalfa fields from June to September in 1999 and 2000. The relationship between each predatory taxa and E. fabae was examined using regression analysis. In 2000, all predators were found to be positively correlated with the presence of E. fabae during all periods sampled and most likely contributed to mortality. Orius insidiosus (Say) (Hemiptera: Anthoridae) was the most numerous insect predatory species; population numbers ranged from 0 to 1 and 0.1 to 3.7 adults per 0.25 m2 in 1999 and 2000, respectively. Partial life tables were constructed for E. fabae nymphs for two alfalfa-growing periods. Nymphs were grouped into three age intervals: first and second, third and fourth, and fifth instars. For the first alfalfa growing period examined, E. fabae nymphal mortality was 70% in 1999 and 49% in 2000. During the last growing period of each season (August–September), total nymphal mortality was relatively low (<25%). Adult E. fabae density ranged from 5.4 to 25.6 and 1.4–9.2 per 0.25 m2 in 1999 and 2000, respectively. E. fabae population peaks were similar for each age interval in all growing periods. This study provides further information on the population dynamics of E. fabae and its relationship with select predatory species in Iowa alfalfa fields. PMID:26320260

  9. Variation for yield, water-use efficiency, and canopy morphology among nine alfalfa germplasms

    International Nuclear Information System (INIS)

    Ray, I.M.; Townsend, M.S.; Henning, J.A.

    1998-01-01

    Alfalfa (Medicago sativa L.) production under irrigated and rainfed conditions may benefit from improvements in water-use efficiency (WUE), the amount of forage and root biomass produced per unit of water transpired. If benefits from improved WUE are to be realized, correlations between important agronomic traits and key physiological traits associated with WUE must be determined. This study characterized variation for dry matter yield, forage maturity, leaf-to-stem ratio (LSR), carbon isotope discrimination (delta), canopy temperature, ash content, and specific leaf mass (SLM) in alfalfa. Associations between traits were also determined. Nine alfalfa germplasms representing eight of the nine historical genetic diversity groups, and a very fall-dormant (VFD) population, were established in seeded, irrigated plots for 2 yr near Las Cruces, NM. Significant variation (P less than or equal to 0.10) was detected for all traits and was greatest for delta and maturity, intermediate for yield, canopy temperature, ash content, and LSR, and least for SLM. The African, Peruvian, and Indian germplasms exhibited a higher delta than either the Turkistan, VFD, M. varia Martyn., or Ladak germplasms. Carbon isotope discrimination was positively correlated with forage yield (r = 0.64; P less than or equal to 0.10; n = 9) and forage maturity (r = 0.66; P less than or equal to 0.05; n = 9). No association was detected between delta and either canopy temperature, ash content, SLM, or LSR. The results indicate that differences in stomatal conductance or photosynthetic capacity exist among the nine populations, and that germplasms with low delta tended to have slower growth and development rates under irrigated conditions. Neither canopy temperature, ash content, nor SLM provided suitable alternate measurements of delta among the nine alfalfa germplasms

  10. Inhibitory potential of pure isoflavonoids, red clover, and alfalfa extracts on hemoglobin glycosylation

    Directory of Open Access Journals (Sweden)

    Mohsen Hosseini

    2015-03-01

    Full Text Available BACKGROUND: Non-enzymatic glycosylation of hemoglobin is complications of diabetes. Antioxidant system imbalance can result in the emergence of free radicals’ destructive effects in the long-term. Red clover (Trifolium pratense L. and alfalfa (Medicago sativa L. contain isoflavonoids and have antioxidant activity. This experimental study evaluated the inhibitory activity of pure isoflavonoids (daidzein and genistein, red clover and alfalfa extracts on hemoglobin glycosylation. METHODS: This study was performed in Iran. Stock solution of hydroalcoholic extracts of red clover and alfalfa in concentrations of 1 and 10 g/100 ml and stock solution of daidzein and genistein in concentrations of 250 ng, 500 ng, 25 µg and 250 µg/100 ml were prepared as case groups. Control group was without hydroalcoholic extracts of plants and pure isoflavonoids. All experiments were performed in triplicate. Hemoglobin was prepared and antioxidant activities were investigated to estimate degree of nonenzymatic hemoglobin glycosylation. RESULTS: There was no significantly difference between used extracts (extract of red clover and alfalfa and control of the hemoglobin glycosylation but using daidzein (P = 0.046, 0.029 and 0.021, respectively and genistein (P = 0.034, 0.036 and 0.028 significantly inhibited (P < 0.050 this reaction in 25 µg/100 ml, 250 and 500 ng/100 ml concentrations when compared to control. in 25 µg/100 ml, 250 ng and 500 ng/100 ml concentrations percentage of inhibition were 32, 80 and 74.5% respectively with used of daidzein and were 21, 83 and 76% respectively with consumption of genistein. CONCLUSION: According to decrease of glycation of hemoglobin with isoflavonoids, two used plant in this study containing isoflavonoid may be useful on diabetes.   

  11. Estimation of the Genetic Diversity in Tetraploid Alfalfa Populations Based on RAPD Markers for Breeding Purposes

    Directory of Open Access Journals (Sweden)

    Slobodan Katic

    2011-08-01

    Full Text Available Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon’s information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm.

  12. Effects of alfalfa hay and its physical form (chopped versus pelleted) on performance of Holstein calves.

    Science.gov (United States)

    Jahani-Moghadam, M; Mahjoubi, E; Hossein Yazdi, M; Cardoso, F C; Drackley, J K

    2015-06-01

    Inclusion of forage and its physical form in starter may affect rumen development, average daily gain (ADG), and dry matter intake (DMI) of dairy calves. To evaluate the effects of forage and its physical form (chopped vs. pelleted) on growth of calves under a high milk feeding regimen, 32 Holstein calves (38.8±1.1kg) were assigned at birth to 1 of 3 treatments in a completely randomized block design. Dietary treatments (% of dry matter) were (1) 100% semi-texturized starter (CON); (2) 90% semi-texturized starter + 10% chopped alfalfa hay (mean particle size=5.4mm) as a total mixed ration (TMR; CH); and (3) 90% semi-texturized starter + 10% pelleted alfalfa (mean=5.8mm) hay as a TMR (PH). Data were subjected to mixed model analysis with contrasts used to evaluate effect of forage inclusion. Calves were weaned at 76 d of age and the experiment finished 2 wk after weaning. Individual milk and solid feed consumption were recorded daily. Solid feed consumption and ADG increased as age increased (effect of week), but neither forage inclusion nor physical form of forage affected these variables pre- or postweaning. Plasma urea N was affected by treatments such that the CON group had a lower concentration than forage-fed groups. Forage inclusion, but not physical form, resulted in increased total protein in plasma. Although days with elevated rectal temperature, fecal score, and general appearance were not affected by dietary treatments, calves fed alfalfa hay during the first month of life had fewer days with respiratory issues, regardless of physical form of hay. We concluded that provision of forage does have some beneficial effects in calves fed large amounts of milk replacer, but pelleted alfalfa hay did not result in any improvement in calf performance or health. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  13. Alterations in membrane protein-profile during cold treatment of alfalfa

    International Nuclear Information System (INIS)

    Mohapatra, S.S.; Poole, R.J.; Dhindsa, R.S.

    1988-01-01

    Changes in pattern of membrane proteins during cold acclimation of alfalfa have been examined. Cold acclimation for 2 to 3 days increases membrane protein content. Labeling of membrane proteins in vivo with [ 35 S]methionine indicates increases in the rate of incorporation as acclimation progresses. Cold acclimation induces the synthesis of about 10 new polypeptides as shown by SDS-PAGE and fluorography of membrane proteins labeled in vivo

  14. Response of cotton, alfalfa, and cantaloupe to foliar-deposited salt in an arid environment

    International Nuclear Information System (INIS)

    Hofmann, W.C.; Karpiscak, M.M.; Bartels, P.G.

    1987-01-01

    The cooling towers at the Palo Verde Nuclear Generating Station (PVNGS), located 80 km west of Phoenix, AZ, will release as estimated 2.1 Mg/d of particulates (primarily salts) into the atmosphere when the station is in full operation. The saline drift will disperse and settle onto agricultural fields surrounding the station. Field studies were conducted in 1983 to investigate the influence of foliar-applied saline aerosol on crop growth, foliar injury, and tissue elemental concentration on cotton (Gossypium hirsutum L.), alfalfa (medicago sativa L.), and cantaloupe (Cucumis melo L.) in an arid environment. The treatment aerosol solutions simulated treated wastewater effluent and included all essential plant nutrients and other elements, including trace concentrations of heavy metals. The treatments included unsprayed plots, and plots sprayed with salt solutions at 0 (distilled water), 8, 83, and 415 kg/(ha yr). The alfalfa received an additional 829 kg/(ha yr) treatment. The species were evaluated in separate experiments on Mohave clay loam and Sonoita sandy loam soils (Typic Haplargid) near Marana, AZ. Cotton treated with 415 kg/(ha yr) had significantly less chlorosis and tended to be slightly taller than the cotton in the unsprayed plots. The alfalfa treated at a rate of 829 kg/(ha yr) showed significantly more leaf margin necrosis than did the unsprayed alfalfa. In the cantaloupe, there were no visually apparent differences among salt treatments. Hand-harvested cotton plots had a significant reduction is seed cotton yield at the 415 kg/(ha yr) treatment. A similar though nonsignificant, trend towards reduced yield with increased salt treatment was observed in machine-harvested cotton plots

  15. Effect of feeding selenium-fertilized alfalfa hay on performance of weaned beef calves.

    Directory of Open Access Journals (Sweden)

    Jean A Hall

    Full Text Available Selenium (Se is an essential micronutrient in cattle, and Se-deficiency can affect morbidity and mortality. Calves may have greater Se requirements during periods of stress, such as during the transitional period between weaning and movement to a feedlot. Previously, we showed that feeding Se-fertilized forage increases whole-blood (WB Se concentrations in mature beef cows. Our current objective was to test whether feeding Se-fertilized forage increases WB-Se concentrations and performance in weaned beef calves. Recently weaned beef calves (n = 60 were blocked by body weight, randomly assigned to 4 groups, and fed an alfalfa hay based diet for 7 wk, which was harvested from fields fertilized with sodium-selenate at a rate of 0, 22.5, 45.0, or 89.9 g Se/ha. Blood samples were collected weekly and analyzed for WB-Se concentrations. Body weight and health status of calves were monitored during the 7-wk feeding trial. Increasing application rates of Se fertilizer resulted in increased alfalfa hay Se content for that cutting of alfalfa (0.07, 0.95, 1.55, 3.26 mg Se/kg dry matter for Se application rates of 0, 22.5, 45.0, or 89.9 g Se/ha, respectively. Feeding Se-fertilized alfalfa hay during the 7-wk preconditioning period increased WB-Se concentrations (P Linear<0.001 and body weights (P Linear = 0.002 depending upon the Se-application rate. Based upon our results we suggest that soil-Se fertilization is a potential management tool to improve Se-status and performance in weaned calves in areas with low soil-Se concentrations.

  16. Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis

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    Zhao Patrick X

    2011-07-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are the most common type of sequence variation among plants and are often functionally important. We describe the use of 454 technology and high resolution melting analysis (HRM for high throughput SNP discovery in tetraploid alfalfa (Medicago sativa L., a species with high economic value but limited genomic resources. Results The alfalfa genotypes selected from M. sativa subsp. sativa var. 'Chilean' and M. sativa subsp. falcata var. 'Wisfal', which differ in water stress sensitivity, were used to prepare cDNA from tissue of clonally-propagated plants grown under either well-watered or water-stressed conditions, and then pooled for 454 sequencing. Based on 125.2 Mb of raw sequence, a total of 54,216 unique sequences were obtained including 24,144 tentative consensus (TCs sequences and 30,072 singletons, ranging from 100 bp to 6,662 bp in length, with an average length of 541 bp. We identified 40,661 candidate SNPs distributed throughout the genome. A sample of candidate SNPs were evaluated and validated using high resolution melting (HRM analysis. A total of 3,491 TCs harboring 20,270 candidate SNPs were located on the M. truncatula (MT 3.5.1 chromosomes. Gene Ontology assignments indicate that sequences obtained cover a broad range of GO categories. Conclusions We describe an efficient method to identify thousands of SNPs distributed throughout the alfalfa genome covering a broad range of GO categories. Validated SNPs represent valuable molecular marker resources that can be used to enhance marker density in linkage maps, identify potential factors involved in heterosis and genetic variation, and as tools for association mapping and genomic selection in alfalfa.

  17. Identification and Selection for Salt Tolerance in Alfalfa (Medicago sativa L. Ecotypes via Physiological Traits

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    Hassan MONIRIFAR

    2009-12-01

    Full Text Available Salt stress is a serious environmental problem throughout the world which may be partially relieved by breeding cultivars that can tolerate salt stress. Plant breeding may provide a relatively cost effective short-term solution to the salinity problem by producing cultivars able to remain productive at low to moderate levels of salinity. Five alfalfa cultivars, �Seyah-Roud�, �Ahar-Hourand�, �Oskou�, �Malekan� and �Sefida-Khan� were assessed for salt tolerance at mature plant stage. A greenhouse screening system was used to evaluate individual alfalfa plants grown in perlit medium, and irrigated with water containing different amounts of NaCl. Three salt levels were achieved by adding 0, 100 and 200 mM NaCl to Hoagland nutrient solution, respectively. Forage yield, sodium and potassium contents and K/Na ratio was determined. Also, leaf samples were analyzed for proline and chlorophyll contents. The ecotypes Seyha-Roud and �Sefida-Khan� had comparatively less sodium contents than �Oskou�, �Ahar-Hourand� and �Malekan� ecotypes, also potassium content increased under saline condition. Forage yield of different alfalfa ecotypes was significantly influenced by the salinity. The ecotypes �Malekan�, Ahar- Hourand and �Oskou� were successful in maintaining forage yield under salinity stress. Sodium contents increased due to salinity in all alfalfa ecotypes however ecotypes �Ahar-Hourand� and �Malekan� maintained the highest leaf Na concentration. They showed higher content of K than other ecotypes but had lower K/Na ratio. It was concluded that, two ecotypes �Malekan� and �Ahar-Hourand� were better.

  18. MODELING POLLINATION FACTORS THAT INFLUENCE ALFALFA SEED YIELD IN NORTH-CENTRAL NEVADA

    OpenAIRE

    BREAZEALE, Don; FERNANDEZ, George; NARAYANAN, Rangesan

    2008-01-01

    The relative importance of both environmental and management factors on alfalfa seed yield was investigated on North–Central Nevada farms. Multiple linear regression models using 2002-2003 data revealed that cumulative tripped fl owers increased seed yield in both years. Field location does not appear to make a difference in the observed variation in tripped fl ower production. The results suggest that seed yield can be increased by (a) by placing bee shelters closer and (b) cultural practice...

  19. 131I levels in cow's milk following ingestion of contaminated alfalfa or sudan grass

    International Nuclear Information System (INIS)

    Black, S.C.; Stanley, R.E.; Barth, D.S.

    1975-08-01

    A dry aerosol, consisting of submicrometer diatomaceous earth particles tagged with 131 I, was released over two different types of growing forage (alfalfa and Sudan grass) at the Experimental Dairy Farm on the Nevada Test Site. Following deposition of the aerosol, the two forage types were chopped and fed to different groups of lactating dairy cows. The dual objectives of the study were to evaluate the relationship of 131 I secretion in milk to the ingestion of different types of contaminated forage and to obtain a further indication of the possible influence on milk radioiodine levels of changing the particle size of the contaminant. The ratios of the peak activity concentrations measured in the milk to the peak activity concentrations in the forage were computed to be 0.0145 for the cows fed contaminated alfalfa and 0.0082 for those fed contaminated Sudan grass. Comparison of the results from this study with those from earlier studies indicates the major effect on activity levels in the milk can be related to forage type. Ingestion of Sudan grass by the cow reduces the transfer of radioiodine to milk by one half compared to ingestion of alfalfa. (U.S.)

  20. Effect of γ-ray irradiation on in vitro culture and plant regeneration of alfalfa

    International Nuclear Information System (INIS)

    Zhang Xiaodong; Lin Tingan

    1992-01-01

    60 Co γ-ray irradiation ranged 0-16 kR was used to treat the cotyledons and hypocotyls of 5 cultivars of a alfalfa (Medicago sativa L.). The effects of irradiation on the frequency of callus, fresh weight of callus, the frequency of somatic embryo induction and plantlet regeneration were studied. The results showed as follows: the radiosensitivities of cotyledon was significantly higher than that of hypocotyl. Exposure of 2 kR could improve the growth of callus, embryogenesis and plantlet regeneration at various levels. Exposure of 12 kR completely inhibited the callus formation from explants of cotyledon. Callus from two cultivars, England 648 and Jining alfalfa, were irradiated with 0-8 kR. The results showed that exposure below 2 kR could promote the growth of callus and the formation of somatic embryo at different levels. The exposure of 8 kR had the effect of lethal. The optimum exposure for genetic improvement of alfalfa in vitro by inducing mutation was considered to be 4-6 kR

  1. Partitioning and mobilization of photoassimilate in alfalfa subjected to water deficits

    International Nuclear Information System (INIS)

    Hall, M.H.; Sheaffer, C.C.; Heichel, G.H.

    1988-01-01

    Faster regrowth of a stressed alfalfa (Medicago sativa L.) crop compared to an unstressed crop after rewatering has been reported. The bases of this compensatory response are unknown, but they may be important to understanding adaptation to water stress and to developing crop water management strategies. The authors objectives was to determine the effect of stress induced by water deficit on photoassimilate partitioning and the utilization of stored assimilates during regrowth of alfalfa. Field and greenhouse experiments were conducted using cultivars differing in winterhardiness. Plants were subjected to water stress, pulse-labeled with 14 CO 2 , and sampled following 0, 1, 14, 21, and 28-d translocation periods. Following the 14-d sampling, herbage was harvested and water stress was removed. Cultivars contrasting in winterhardiness responded similarly to water stress. Stressed plant roots contained 73 and 114% more total plant radioactivity (TPR) than the control at the 1 and 14-d translocation periods, respectively. Water stress significantly increased root starch and TPR percentage in the starch fraction, but had much smaller effects on root soluble-sugar concentration and TPR percentage of the root sugar fraction. Herbage regrowth mass following harvest and rewatering of the water-stressed plants was similar to that of the control. Compared to the control, water-stressed alfalfa has greater total nonstructural carbohydrates in the roots, apparently due to increased photoassimilate partitioning to the roots. However, the greater root carbohydrate concentrations did not result in compensatory herbage regrowth following rewatering

  2. Effect of Non Thermal Plasma on Alfalfa (Medicago sativa L.) Forage Production

    International Nuclear Information System (INIS)

    Abd El-Daem, G.A.N.A.; El-Aragi, G.M.; Tarrad, M.M.; Zayed, E.M.

    2013-01-01

    Field experiments were conducted at Atomic Energy Authority (AEA) Farm, at Inshas, Egypt during 2011–2012 on alfalfa. The aim of this investigation to caused mutation in alfalfa to obtain new variation. Seeds of the alfalfa were subjected to six doses of non-thermal plasma pulse. The plasma (consisting of ozone, UV and visible light) was injected into the seed samples for different durations or number of pulses. The doses used treatments were 2, 4, 6, 8, and 10 pulses (P) and non-treated control. The results showed difference seeds in both level field performances from cut 1st to cut 10th in the forage production. The results showed differences between the Control and treatment (number of pulses (P)) in each of all cuts for the productivity. The results showed the impact of plant height, Number of leaves/plant and number of branches/leaf and stem diameter as well as fresh weight of plant, fresh/weight (t/fed), dry yield (t/fed) in some cuts for Pulses 2, 4 and 10, and the ten pulses were the best for the majority of the qualities and cuts.

  3. Ruminal changes in monensin- and lasalocid-fed cattle grazing bloat-provocative alfalfa pasture.

    Science.gov (United States)

    Katz, M P; Nagaraja, T G; Fina, L R

    1986-10-01

    Microbial and fermentation changes in the rumen in monensin- and lasalocid-fed cattle grazing bloat-provocative alfalfa pasture were studied using genetically bloat-susceptible, ruminally-cannulated adult cattle. Monensin at .66 and .99 mg/kg body weight daily reduced the severity of legume bloat by 41 and 73%, respectively. The same doses of lasalocid reduced bloat by 25 and 12%. Comparison of ruminal contents from animals before treatment with ruminal contents from antibiotic-treated animals showed no differences in pH, ammonia, soluble N, soluble carbohydrate, ethanol-precipitable slime and anaerobic bacterial counts. Monensin treatment decreased protozoal numbers and microbial activity, as evidenced by lower gas production from in vitro fermentation of ground alfalfa hay when compared to pretreatment. Lasalocid had no effect on protozoal counts and in vitro gas production. Addition of monensin or lasalocid (12 micrograms/ml) to in vitro fermentation of chopped, fresh alfalfa reduced microbial activity as evidenced by higher soluble N, lower ammonia concentration and decreased gas production. Monensin reduced the amount of ethanol-precipitable slime and protozoal numbers. Reduction in the severity of bloat when monensin was fed appears to be due to decreased protozoal numbers, which resulted in decreased gas production. Lasalocid did not reduce legume bloat because of its minimal effect on the ruminal protozoa.

  4. Application limestone forms and doses for alfalfa in no-tillage system

    Directory of Open Access Journals (Sweden)

    Letícia Cristina Bertusso Toffolli

    Full Text Available Alfalfa (Medicago sativa L. requires good soil fertility. Brazil is characterized by acidic soils which reduce the potential of the crop. Generally, liming is incorporated into the soil, but in tillage systems it is inadvisable. This study aimed to evaluate the effects of the lime application method and dose on pH, Al+3, V % and Ca+Mg in the soil and on dry matter yield of alfalfa cultivated under a consolidated no-tillage system. The experiment was conducted at the Experimental Station of Paraná Agronomic Institute, located in Pato Branco city, in Paraná state. The plots consisted of the types of lime application (plowing+harrowing, subsoil and surface, the sub-plots was the lime dose (0, 2, 4, 6 and 8 Mg ha-1 and the sub-sub-plots were the sampled soil depth (0-5; 5-10; 10-20 and 20-30 cm. The results show the application of lime, even superficially, caused increases in pH, concentration of Ca and Mg and base saturation of the soil, while also reducing the concentration of Al, especially in the surface layers of the soil. The practice of plowing and harrowing or of subsoiling, with the aim of lime incorporation in a consolidated no-tillage system is unnecessary. If it is required, the application of lime to the soil should be done superficially for alfalfa cultivated in this system.

  5. Effects of heterosis for yield and yield components obtained by crossing divergent alfalfa populations

    Directory of Open Access Journals (Sweden)

    Katić Slobodan

    2010-01-01

    Full Text Available When breeding alfalfa for yield performance, it is necessary to use high-yielding parents obtained by different breeding methods. The assumption at the onset of this research was that crossing highest-yielding domestic cultivars with divergent populations from geographically distant breeding centers could result in the expression of heterotic effects in their hybrids contributing to increased alfalfa yield. The objective of this study was to determine yield and yield components and heterotic effects in hybrid progenies obtained by crossing the domestic cultivars NS Banat ZMS II and NS Mediana ZMS V with the cultivars Pella, Dolichi and Hyliki from Greece, UMSS 2001 from Bolivia and Jogeva 118 from Estonia in two series. The field trial planted in 2006, included 13 F1 hybrids and 6 of 7 initial parents in both series. Heterotic effects for yields of forage and hay were observed in 4 combinations (C NS Banat ZMS II x E Hyliki; C NS Banat ZMS II x E UMSS 2001; C NS Mediana ZMS V x E Hyliki; C NS Mediana ZMS V x E Dolichi. The populations that exhibited heterosis in a set of crossings are recommended for use as parent components for development of high-yielding synthetic alfalfa cultivars. .

  6. [Composition diversity of lactic acid bacteria (LAB) community Al2 used for alfalfa silage].

    Science.gov (United States)

    Wang, Xiao-Fen; Gao, Li-Juan; Yang, Hong-Yan; Wang, Wei-Dong; Cui, Zong-Jun

    2006-10-01

    Alfalfa is the most important forage grass that is difficult to ensile for good quality. Using silage inoculants are the important way for preservation of alfalfa silage. Through continuous restricted subcultivation, a lactic acid bacteria (LAB) community Al2 was selected from well-fermented alfalfa silage. Plate isolation and Denaturing Gradient Gel Electrophoresis (DGGE), construction of 16S rDNA clone library were used to identify the composition diversity of Al2 community, with 7 strains detected, and they were all belonged to Lactobacillus. The composition ratios of the 7 strains were 55.21%, 19.79%, 14.58%, 3.13%, 3.13%, 3.13%, 1.03% according to 16S rDNA clone library. Al2-1i, Al2-2i, Al2-3i, corresponding to L. plantarum (99.9%), L. kimchii (99.4%), L. farciminis (100%) were detected by plate isolation. Among 3 isolates, Al2-1i had the highest ability of dropping pH and producing lactic acid, and the amount of lactic acid was reach to 18g/L at 24h cultivated in MRS media. The ability of dropping pH and producing lactic acid of Al2-3i was the lowest. From DGGE profiles, the dominant strains in Al2 community were L. plantarum and L. kimchii. L. plantarum was detected during the whole process, and L. kimchii was detected in the later phase.

  7. Enhanced salt tolerance of alfalfa (Medicago sativa) by rstB gene transformation.

    Science.gov (United States)

    Zhang, Wan-Jun; Wang, Tao

    2015-05-01

    Generating salt tolerance forage plant is essential for use of the land affected by high salinity. A salt tolerance gene rstB was used as a selectable marker gene in Agrobacterium-mediated transformation of tobacco under a selective regime of 170mM NaCl. The transgenic plants showed clear improvement in salt tolerance. To improve salt tolerance of alfalfa (Medicago sativa L.), rstB gene was introduced into alfalfa genome by Agrobacterium-mediated transformation. No abnormal phenotype was observed among the transgenic plants when compared with wild type (wt) plants. Significant enhancement of resistance to salt-shock treatment was noted on the rstB transgenic (T0) plants. Transgenic second-generation (T1) seeds showed improved germination rate and seedling growth under salt-stress condition. Hindered Na(+) accumulation, but enhanced Ca(2+) accumulation was observed on the rstB T1 plants when subjected to salt-stresses. Enhanced calcium accumulation in transgenic plants was also verified by cytohistochemical localization of calcium. Under salt-stress of 50mM NaCl, about 15% of the transgenic plants finished their life-cycle but the wt plants had no flower formation. The results demonstrated that the expression of rstB gene improved salt tolerance in transgenic alfalfa. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  8. Responses to ozone pollution of alfalfa exposed to increasing salinity levels

    Energy Technology Data Exchange (ETDEWEB)

    Maggio, Albino; Chiaranda, Fabrizio Quaglietta; Cefariello, Roberto [DIAAT, Naples University Federico II, via Universita 100, 80055 Portici (Italy); Fagnano, Massimo, E-mail: fagnano@unina.i [DIAAT, Naples University Federico II, via Universita 100, 80055 Portici (Italy)

    2009-05-15

    Stomatal closure and biosynthesis of antioxidant molecules are two fundamental components of the physiological machinery that lead to stress adaptation during plant's exposure to salinity. Since high stomatal resistance may also contribute in counteracting O{sub 3} damages, we hypothesized that soil salinization may increase O{sub 3} tolerance of crops. An experiment was performed with alfalfa grown in filtered (AOT40 = 0 in both years) and non-filtered (AOT40 = 9.7 in 2005 and 6.9 ppm h in 2006) open-top chambers. Alfalfa yield was reduced by O{sub 3} (-33%) only in plants irrigated with salt-free water, while the increasing levels of soil salinity until 1.06 dS m{sup -1} reduced both stomatal conductance and plant O{sub 3} uptake, thus linearly reducing O{sub 3} effects on yield. Therefore a reliable flux-based model for assessing the effects of O{sub 3} on crop yield should take into account soil salinity. - Moderate saline stress can reduce ozone uptake and yield losses in alfalfa plants.

  9. Concurrent synthesis and release of nod-gene-inducing flavonoids from alfalfa roots

    International Nuclear Information System (INIS)

    Maxwell, C.A.; Phillips, D.A.

    1990-01-01

    Flavonoid signals from alfalfa (Medicago sativa L.) induce transcription of nodulation (nod) genes in Rhizobium meliloti. Alfalfa roots release three major nod-gene inducers: 4',7-dihydroxyflavanone, 4',7-dihydroxyflavone, and 4,4'-dihydroxy-2'-methoxychalcone. The objective of the present study was to define temporal relationships between synthesis and exudation for those flavonoids. Requirements for concurrent flavonoid biosynthesis were assessed by treating roots of intact alfalfa seedlings with [U- 14 C]-L-phenylalanine in the presence or absence of the phenylalanine ammonia-lyase inhibitor L-2-aminoxy-3-phenylpropionic acid (AOPP). In the absence of AOPP, each of the three flavonoids in exudates contained 14 C. In the presence of AOPP, 14 C labeling and release of all the exuded nod-gene inducers were reduced significantly. AOPP inhibited labeling and release of the strongest nod-gene inducer, methoxychalcone, by more than 90%. The release process responsible for exudation of nod-gene inducers appears to be specific rather than a general phenomenon such as a sloughing off of cells during root growth

  10. Responses to ozone pollution of alfalfa exposed to increasing salinity levels

    International Nuclear Information System (INIS)

    Maggio, Albino; Chiaranda, Fabrizio Quaglietta; Cefariello, Roberto; Fagnano, Massimo

    2009-01-01

    Stomatal closure and biosynthesis of antioxidant molecules are two fundamental components of the physiological machinery that lead to stress adaptation during plant's exposure to salinity. Since high stomatal resistance may also contribute in counteracting O 3 damages, we hypothesized that soil salinization may increase O 3 tolerance of crops. An experiment was performed with alfalfa grown in filtered (AOT40 = 0 in both years) and non-filtered (AOT40 = 9.7 in 2005 and 6.9 ppm h in 2006) open-top chambers. Alfalfa yield was reduced by O 3 (-33%) only in plants irrigated with salt-free water, while the increasing levels of soil salinity until 1.06 dS m -1 reduced both stomatal conductance and plant O 3 uptake, thus linearly reducing O 3 effects on yield. Therefore a reliable flux-based model for assessing the effects of O 3 on crop yield should take into account soil salinity. - Moderate saline stress can reduce ozone uptake and yield losses in alfalfa plants.

  11. Micromonospora from nitrogen fixing nodules of alfalfa (Medicago sativa L.). A new promising Plant Probiotic Bacteria.

    Science.gov (United States)

    Martínez-Hidalgo, Pilar; Galindo-Villardón, Purificación; Trujillo, Martha E; Igual, José M; Martínez-Molina, Eustoquio

    2014-09-17

    Biotic interactions can improve agricultural productivity without costly and environmentally challenging inputs. Micromonospora strains have recently been reported as natural endophytes of legume nodules but their significance for plant development and productivity has not yet been established. The aim of this study was to determine the diversity and function of Micromonospora isolated from Medicago sativa root nodules. Micromonospora-like strains from field alfalfa nodules were characterized by BOX-PCR fingerprinting and 16S rRNA gene sequencing. The ecological role of the interaction of the 15 selected representative Micromonospora strains was tested in M. sativa. Nodulation, plant growth and nutrition parameters were analyzed. Alfalfa nodules naturally contain abundant and highly diverse populations of Micromonospora, both at the intra- and at interspecific level. Selected Micromonospora isolates significantly increase the nodulation of alfalfa by Ensifer meliloti 1021 and also the efficiency of the plant for nitrogen nutrition. Moreover, they promote aerial growth, the shoot-to-root ratio, and raise the level of essential nutrients. Our results indicate that Micromonospora acts as a Rhizobia Helper Bacteria (RHB) agent and has probiotic effects, promoting plant growth and increasing nutrition efficiency. Its ecological role, biotechnological potential and advantages as a plant probiotic bacterium (PPB) are also discussed.

  12. Correlations between environmental factors and wild bee behavior on alfalfa (Medicago sativa) in northwestern China.

    Science.gov (United States)

    Wang, Xiaojuan; Liu, Hongping; Li, Xiaoxia; Song, Yu; Chen, Li; Jin, Liang

    2009-10-01

    To discover the effect of environmental factors on pollinator visitation to flowering Medicago sativa, several field experiments were designed to examine the diurnal movement patterns of wild bee species in the Hexi Corridor of northwestern China. Our study results showed that Megachile abluta, M. spissula, and Xylocopa valga showed unimodal diurnal foraging behavior, whereas Andrena parvula and Anthophora melanognatha showed bimodal diurnal foraging behavior. Correlation analysis indicated that diurnal foraging activities of pollinators were significantly correlated with environmental factors. Correlations of foraging activities versus environmental factors for M. abluta, M. spissula, and X. valga best fit a linear model, whereas those of A. parvula and A. melanognatha best fit a parallel quadratic model. Results of this study indicated that solitary wild bees such as M. abluta, M. spissula, X. valga, A. parvula, and A. melanognatha are potential alfalfa pollinators in the Hexi Corridor. An understanding of the environmental factors that affect the behaviors of different wild bees foraging in alfalfa are basic to the utilization of solitary wild bees in a practical way for increased, or more consistent, pollination of alfalfa for seed production.

  13. Diurnal behavior of dairy cows on alfalfa pastures supplemented with corn silage and concentrate

    Directory of Open Access Journals (Sweden)

    D. Peres Netto

    2014-06-01

    Full Text Available The diurnal ingestive behavior of dairy cows on alfalfa pastures supplemented with corn silage and concentrate was evaluated. Sixteen Holstein dairy cows in mid-lactation were used in a randomized block design. The treatments were partial replacement of corn silage for limited alfalfa grazing time (LGT or unlimited grazing time (UGT. Rotational alfalfa grazing was used and the amount of concentrate fed was the same in both treatments. Behavioral activities observed were time spent grazing, rumination and idleness, during four days, from 8:00 AM to 7:00 PM. From 2:00 to 5:00 PM grazing was intermittent and short-lasting on UGT, whereas on LGT grazing activity was longer than UGT in the morning and at the end of the afternoon. Restriction in available grazing time clearly influenced the distribution of time spent with grazing, rumination and idleness throughout the day. However, this effect was not observed in the total time spent in these activities.

  14. The roles of WRN and BLM RecQ helicases in the Alternative Lengthening of Telomeres.

    Science.gov (United States)

    Mendez-Bermudez, Aaron; Hidalgo-Bravo, Alberto; Cotton, Victoria E; Gravani, Athanasia; Jeyapalan, Jennie N; Royle, Nicola J

    2012-11-01

    Approximately 10% of all cancers, but a higher proportion of sarcomas, use the recombination-based alternative lengthening of telomeres (ALT) to maintain telomeres. Two RecQ helicase genes, BLM and WRN, play important roles in homologous recombination repair and they have been implicated in telomeric recombination activity, but their precise roles in ALT are unclear. Using analysis of sequence variation present in human telomeres, we found that a WRN- ALT+ cell line lacks the class of complex telomere mutations attributed to inter-telomeric recombination in other ALT+ cell lines. This suggests that WRN facilitates inter-telomeric recombination when there are sequence differences between the donor and recipient molecules or that sister-telomere interactions are suppressed in the presence of WRN and this promotes inter-telomeric recombination. Depleting BLM in the WRN- ALT+ cell line increased the mutation frequency at telomeres and at the MS32 minisatellite, which is a marker of ALT. The absence of complex telomere mutations persisted in BLM-depleted clones, and there was a clear increase in sequence homogenization across the telomere and MS32 repeat arrays. These data indicate that BLM suppresses unequal sister chromatid interactions that result in excessive homogenization at MS32 and at telomeres in ALT+ cells.

  15. A rapid Salmonella detection method involving thermophilic helicase-dependent amplification and a lateral flow assay.

    Science.gov (United States)

    Du, Xin-Jun; Zhou, Tian-Jiao; Li, Ping; Wang, Shuo

    2017-08-01

    Salmonella is a major foodborne pathogen that is widespread in the environment and can cause serious human and animal disease. Since conventional culture methods to detect Salmonella are time-consuming and laborious, rapid and accurate techniques to detect this pathogen are critically important for food safety and diagnosing foodborne illness. In this study, we developed a rapid, simple and portable Salmonella detection strategy that combines thermophilic helicase-dependent amplification (tHDA) with a lateral flow assay to provide a detection result based on visual signals within 90 min. Performance analyses indicated that the method had detection limits for DNA and pure cultured bacteria of 73.4-80.7 fg and 35-40 CFU, respectively. Specificity analyses showed no cross reactions with Escherichia coli, Staphylococcus aureus, Listeria monocytogenes, Enterobacter aerogenes, Shigella and Campylobacter jejuni. The results for detection in real food samples showed that 1.3-1.9 CFU/g or 1.3-1.9 CFU/mL of Salmonella in contaminated chicken products and infant nutritional cereal could be detected after 2 h of enrichment. The same amount of Salmonella in contaminated milk could be detected after 4 h of enrichment. This tHDA-strip can be used for the rapid detection of Salmonella in food samples and is particularly suitable for use in areas with limited equipment. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Antiviral drug resistance and helicase-primase inhibitors of herpes simplex virus.

    Science.gov (United States)

    Field, Hugh J; Biswas, Subhajit

    2011-02-01

    A new class of chemical inhibitors has been discovered that interferes with the process of herpesvirus DNA replication. To date, the majority of useful herpesvirus antivirals are nucleoside analogues that block herpesvirus DNA replication by targeting the DNA polymerase. The new helicase-primase inhibitors (HPI) target a different enzyme complex that is also essential for herpesvirus DNA replication. This review will place the HPI in the context of previous work on the nucleoside analogues. Several promising highly potent HPI will be described with a particular focus on the identification of drug-resistance mutations. Several HPI have good pharmacological profiles and are now at the outset of phase II clinical trials. Provided there are no safety issues to stop their progress, this new class of compound will be a major advance in the herpesvirus antiviral field. Furthermore, HPI are likely to have a major impact on the therapy and prevention of herpes simplex virus and varicella zoster in both immunocompetent and immunocompromised patients alone or in combination with current nucleoside analogues. The possibility of acquired drug-resistance to HPI will then become an issue of great practical importance. Copyright © 2010 Elsevier Ltd. All rights reserved.

  17. DNA replication restart and cellular dynamics of Hef helicase/nuclease protein in Haloferax volcanii.

    Science.gov (United States)

    Lestini, Roxane; Delpech, Floriane; Myllykallio, Hannu

    2015-11-01

    Understanding how frequently spontaneous replication arrests occur and how archaea deal with these arrests are very interesting and challenging research topics. Here we will described how genetic and imaging studies have revealed the central role of the archaeal helicase/nuclease Hef belonging to the XPF/MUS81/FANCM family of endonucleases in repair of arrested replication forks. Special focus will be on description of a recently developed combination of genetic and imaging tools to study the dynamic localization of a functional Hef::GFP (Green Fluorescent Protein) fusion protein in the living cells of halophilic archaea Haloferax volcanii. As Archaea provide an excellent and unique model for understanding how DNA replication is regulated to allow replication of a circular DNA molecule either from single or multiple replication origins, we will also summarize recent studies that have revealed peculiar features regarding DNA replication, particularly in halophilic archaea. We strongly believe that fundamental knowledge of our on-going studies will shed light on the evolutionary history of the DNA replication machinery and will help to establish general rules concerning replication restart and the key role of recombination proteins not only in bacteria, yeast and higher eukaryotes but also in archaea. Copyright © 2015 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  18. Mutation and Methylation Analysis of the Chromodomain-Helicase-DNA Binding 5 Gene in Ovarian Cancer

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    Kylie L. Gorringe

    2008-11-01

    Full Text Available Chromodomain, helicase, DNA binding 5 (CHD5 is a member of a subclass of the chromatin remodeling Swi/Snf proteins and has recently been proposed as a tumor suppressor in a diverse range of human cancers. We analyzed all 41 coding exons of CHD5 for somatic mutations in 123 primary ovarian cancers as well as 60 primary breast cancers using high-resolution melt analysis. We also examined methylation of the CHD5 promoter in 48 ovarian cancer samples by methylation-specific single-stranded conformation polymorphism and bisulfite sequencing. In contrast to previous studies, no mutations were identified in the breast cancers, but somatic heterozygous missense mutations were identified in 3 of 123 ovarian cancers. We identified promoter methylation in 3 of 45 samples with normal CHD5 and in 2 of 3 samples with CHD5 mutation, suggesting these tumors may have biallelic inactivation of CHD5. Hemizygous copy number loss at CHD5 occurred in 6 of 85 samples as assessed by single nucleotide polymorphism array. Tumors with CHD5 mutation or methylation were more likely to have mutation of KRAS or BRAF (P = .04. The aggregate frequency of CHD5 haploinsufficiency or inactivation is 16.2% in ovarian cancer. Thus, CHD5 may play a role as a tumor suppressor gene in ovarian cancer; however, it is likely that there is another target of the frequent copy number neutral loss of heterozygosity observed at 1p36.

  19. Helicase Dependent Isothermal Amplification of DNA and RNA using Self-Avoiding Molecular Recognition Systems

    Science.gov (United States)

    Yang, Zunyi; McLendon, Chris; Hutter, Daniel; Bradley, Kevin M.; Hoshika, Shuichi; Frye, Carole; Benner, Steven A.

    2015-01-01

    Assays that target DNA or RNA (xNA) are highly sensitive, as small amounts of xNA can be amplified by PCR. Unfortunately, PCR is inconvenient in low resource environments, requiring equipment and power that may not be available in these environments. However, isothermal procedures that avoid thermal cycling are often confounded by primer dimers, off-target priming, and other artifacts. Here, we show how a “self avoiding molecular recognition system” (SAMRS) eliminates these artifacts to give clean amplicons in a helicase-dependent isothermal amplification (SAMRS-HDA). We also show that incorporating SAMRS into the 3′-ends of primers facilitates the design and screening of primers for HDA assays. Finally, we show that SAMRS-HDA can be twofold multiplexed, something difficult to achieve with HDA using standard primers. This shows that SAMRS-HDA is a more versatile approach than standard HDA with a broader applicability for xNA-targeted diagnostics and research. PMID:25953623

  20. AAA-ATPase FIDGETIN-LIKE 1 and Helicase FANCM Antagonize Meiotic Crossovers by Distinct Mechanisms.

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    Chloe Girard

    2015-07-01

    Full Text Available Meiotic crossovers (COs generate genetic diversity and are critical for the correct completion of meiosis in most species. Their occurrence is tightly constrained but the mechanisms underlying this limitation remain poorly understood. Here we identified the conserved AAA-ATPase FIDGETIN-LIKE-1 (FIGL1 as a negative regulator of meiotic CO formation. We show that Arabidopsis FIGL1 limits CO formation genome-wide, that FIGL1 controls dynamics of the two conserved recombinases DMC1 and RAD51 and that FIGL1 hinders the interaction between homologous chromosomes, suggesting that FIGL1 counteracts DMC1/RAD51-mediated inter-homologue strand invasion to limit CO formation. Further, depleting both FIGL1 and the previously identified anti-CO helicase FANCM synergistically increases crossover frequency. Additionally, we showed that the effect of mutating FANCM on recombination is much lower in F1 hybrids contrasting from the phenotype of inbred lines, while figl1 mutation equally increases crossovers in both contexts. This shows that the modes of action of FIGL1 and FANCM are differently affected by genomic contexts. We propose that FIGL1 and FANCM represent two successive barriers to CO formation, one limiting strand invasion, the other disassembling D-loops to promote SDSA, which when both lifted, leads to a large increase of crossovers, without impairing meiotic progression.

  1. The DEAD box helicase RDE-12 promotes amplification of RNAi in cytoplasmic foci in C. elegans.

    Science.gov (United States)

    Yang, Huan; Vallandingham, Jim; Shiu, Philip; Li, Hua; Hunter, Craig P; Mak, Ho Yi

    2014-04-14

    RNAi is a potent mechanism for downregulating gene expression. Conserved RNAi pathway components are found in animals, plants, fungi, and other eukaryotes. In C. elegans, the RNAi response is greatly amplified by the synthesis of abundant secondary small interfering RNAs (siRNAs). Exogenous double-stranded RNA is processed by Dicer and RDE-1/Argonaute into primary siRNA that guides target mRNA recognition. The RDE-10/RDE-11 complex and the RNA-dependent RNA polymerase RRF-1 then engage the target mRNA for secondary siRNA synthesis. However, the molecular link between primary siRNA production and secondary siRNA synthesis remains largely unknown. Furthermore, it is unclear whether the subcellular sites for target mRNA recognition and degradation coincide with sites where siRNA synthesis and amplification occur. In the C. elegans germline, cytoplasmic P granules at the nuclear pores and perinuclear Mutator foci contribute to target mRNA surveillance and siRNA amplification, respectively. We report that RDE-12, a conserved phenylalanine-glycine (FG) domain-containing DEAD box helicase, localizes in P granules and cytoplasmic foci that are enriched in RSD-6 but are excluded from the Mutator foci. Our results suggest that RDE-12 promotes secondary siRNA synthesis by orchestrating the recruitment of RDE-10 and RRF-1 to primary siRNA-targeted mRNA in distinct cytoplasmic compartments. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Phosphopeptide binding by Sld3 links Dbf4-dependent kinase to MCM replicative helicase activation.

    Science.gov (United States)

    Deegan, Tom D; Yeeles, Joseph Tp; Diffley, John Fx

    2016-05-02

    The initiation of eukaryotic DNA replication requires the assembly of active CMG (Cdc45-MCM-GINS) helicases at replication origins by a set of conserved and essential firing factors. This process is controlled during the cell cycle by cyclin-dependent kinase (CDK) and Dbf4-dependent kinase (DDK), and in response to DNA damage by the checkpoint kinase Rad53/Chk1. Here we show that Sld3, previously shown to be an essential CDK and Rad53 substrate, is recruited to the inactive MCM double hexamer in a DDK-dependent manner. Sld3 binds specifically to DDK-phosphorylated peptides from two MCM subunits (Mcm4, 6) and then recruits Cdc45. MCM mutants that cannot bind Sld3 or Sld3 mutants that cannot bind phospho-MCM or Cdc45 do not support replication. Moreover, phosphomimicking mutants in Mcm4 and Mcm6 bind Sld3 without DDK and facilitate DDK-independent replication. Thus, Sld3 is an essential "reader" of DDK phosphorylation, integrating signals from three distinct protein kinase pathways to coordinate DNA replication during S phase. © 2016 The Authors. Published under the terms of the CC BY 4.0 license.

  3. Functional Dynamics of Hexameric Helicase Probed by Hydrogen Exchange and Simulation

    Science.gov (United States)

    Radou, Gaël; Dreyer, Frauke N.; Tuma, Roman; Paci, Emanuele

    2014-01-01

    The biological function of large macromolecular assemblies depends on their structure and their dynamics over a broad range of timescales; for this reason, it is a significant challenge to investigate these assemblies using conventional experimental techniques. One of the most promising experimental techniques is hydrogen-deuterium exchange detected by mass spectrometry. Here, we describe to our knowledge a new computational method for quantitative interpretation of deuterium exchange kinetics and apply it to a hexameric viral helicase P4 that unwinds and translocates RNA into a virus capsid at the expense of ATP hydrolysis. Room-temperature dynamics probed by a hundred nanoseconds of all-atom molecular dynamics simulations is sufficient to predict the exchange kinetics of most sequence fragments and provide a residue-level interpretation of the low-resolution experimental results. The strategy presented here is also a valuable tool to validate experimental data, e.g., assignments, and to probe mechanisms that cannot be observed by x-ray crystallography, or that occur over timescales longer than those that can be realistically simulated, such as the opening of the hexameric ring. PMID:25140434

  4. Helicase-primase inhibitor amenamevir for herpesvirus infection: Towards practical application for treating herpes zoster.

    Science.gov (United States)

    Shiraki, K

    2017-11-01

    Valacyclovir and famciclovir enabled successful systemic therapy for treating herpes simplex virus (HSV) and varicella zoster virus (VZV) infection by their phosphorylation with viral thymidine kinase. Helicase-primase inhibitors (HPIs) inhibit the progression of the replication fork, an initial step in DNA synthesis to separate the double strand into two single strands. The HPIs amenamevir and pritelivir have a novel mechanism of action, once-daily administration with nonrenal excretory characteristics, and clinical efficacy for genital herpes. Amenamevir exhibits anti-VZV and anti-HSV activity while pritelivir only has anti-HSV activity. A clinical trial of amenamevir for herpes zoster has been completed, and amenamevir has been licensed and successfully used in 20,000 patients with herpes zoster so far in Japan. We have characterized the features of the antiviral action of amenamevir and, unlike acyclovir, the drug's antiviral activity is not influenced by the viral replication cycle. Amenamevir is opening a new era of antiherpes therapy. Copyright 2017 Clarivate Analytics.

  5. Inherited mutations in the helicase RTEL1 cause telomere dysfunction and Hoyeraal-Hreidarsson syndrome.

    Science.gov (United States)

    Deng, Zhong; Glousker, Galina; Molczan, Aliah; Fox, Alan J; Lamm, Noa; Dheekollu, Jayaraju; Weizman, Orr-El; Schertzer, Michael; Wang, Zhuo; Vladimirova, Olga; Schug, Jonathan; Aker, Memet; Londoño-Vallejo, Arturo; Kaestner, Klaus H; Lieberman, Paul M; Tzfati, Yehuda

    2013-09-03

    Telomeres repress the DNA damage response at the natural chromosome ends to prevent cell-cycle arrest and maintain genome stability. Telomeres are elongated by telomerase in a tightly regulated manner to ensure a sufficient number of cell divisions throughout life, yet prevent unlimited cell division and cancer development. Hoyeraal-Hreidarsson syndrome (HHS) is characterized by accelerated telomere shortening and a broad range of pathologies, including bone marrow failure, immunodeficiency, and developmental defects. HHS-causing mutations have previously been found in telomerase and the shelterin component telomeric repeat binding factor 1 (TRF1)-interacting nuclear factor 2 (TIN2). We identified by whole-genome exome sequencing compound heterozygous mutations in four siblings affected with HHS, in the gene encoding the regulator of telomere elongation helicase 1 (RTEL1). Rtel1 was identified in mouse by its genetic association with telomere length. However, its mechanism of action and whether it regulates telomere length in human remained unknown. Lymphoblastoid cell lines obtained from a patient and from the healthy parents carrying heterozygous RTEL1 mutations displayed telomere shortening, fragility and fusion, and growth defects in culture. Ectopic expression of WT RTEL1 suppressed the telomere shortening and growth defect, confirming the causal role of the RTEL1 mutations in HHS and demonstrating the essential function of human RTEL1 in telomere protection and elongation. Finally, we show that human RTEL1 interacts with the shelterin protein TRF1, providing a potential recruitment mechanism of RTEL1 to telomeres.

  6. Inherited mutations in the helicase RTEL1 cause telomere dysfunction and Hoyeraal–Hreidarsson syndrome

    Science.gov (United States)

    Deng, Zhong; Glousker, Galina; Molczan, Aliah; Fox, Alan J.; Lamm, Noa; Dheekollu, Jayaraju; Weizman, Orr-El; Schertzer, Michael; Wang, Zhuo; Vladimirova, Olga; Schug, Jonathan; Aker, Memet; Londoño-Vallejo, Arturo; Kaestner, Klaus H.; Lieberman, Paul M.; Tzfati, Yehuda

    2013-01-01

    Telomeres repress the DNA damage response at the natural chromosome ends to prevent cell-cycle arrest and maintain genome stability. Telomeres are elongated by telomerase in a tightly regulated manner to ensure a sufficient number of cell divisions throughout life, yet prevent unlimited cell division and cancer development. Hoyeraal–Hreidarsson syndrome (HHS) is characterized by accelerated telomere shortening and a broad range of pathologies, including bone marrow failure, immunodeficiency, and developmental defects. HHS-causing mutations have previously been found in telomerase and the shelterin component telomeric repeat binding factor 1 (TRF1)-interacting nuclear factor 2 (TIN2). We identified by whole-genome exome sequencing compound heterozygous mutations in four siblings affected with HHS, in the gene encoding the regulator of telomere elongation helicase 1 (RTEL1). Rtel1 was identified in mouse by its genetic association with telomere length. However, its mechanism of action and whether it regulates telomere length in human remained unknown. Lymphoblastoid cell lines obtained from a patient and from the healthy parents carrying heterozygous RTEL1 mutations displayed telomere shortening, fragility and fusion, and growth defects in culture. Ectopic expression of WT RTEL1 suppressed the telomere shortening and growth defect, confirming the causal role of the RTEL1 mutations in HHS and demonstrating the essential function of human RTEL1 in telomere protection and elongation. Finally, we show that human RTEL1 interacts with the shelterin protein TRF1, providing a potential recruitment mechanism of RTEL1 to telomeres. PMID:23959892

  7. Translational control by the DEAD Box RNA helicase belle regulates ecdysone-triggered transcriptional cascades.

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    Robert J Ihry

    Full Text Available Steroid hormones act, through their respective nuclear receptors, to regulate target gene expression. Despite their critical role in development, physiology, and disease, however, it is still unclear how these systemic cues are refined into tissue-specific responses. We identified a mutation in the evolutionarily conserved DEAD box RNA helicase belle/DDX3 that disrupts a subset of responses to the steroid hormone ecdysone during Drosophila melanogaster metamorphosis. We demonstrate that belle directly regulates translation of E74A, an ets transcription factor and critical component of the ecdysone-induced transcriptional cascade. Although E74A mRNA accumulates to abnormally high levels in belle mutant tissues, no E74A protein is detectable, resulting in misregulation of E74A-dependent ecdysone response genes. The accumulation of E74A mRNA in belle mutant salivary glands is a result of auto-regulation, fulfilling a prediction made by Ashburner nearly 40 years ago. In this model, Ashburner postulates that, in addition to regulating secondary response genes, protein products of primary response genes like E74A also inhibit their own ecdysone-induced transcription. Moreover, although ecdysone-triggered transcription of E74A appears to be ubiquitous during metamorphosis, belle-dependent translation of E74A mRNA is spatially restricted. These results demonstrate that translational control plays a critical, and previously unknown, role in refining transcriptional responses to the steroid hormone ecdysone.

  8. Mycobacterium smegmatis Lhr Is a DNA-dependent ATPase and a 3'-to-5' DNA translocase and helicase that prefers to unwind 3'-tailed RNA:DNA hybrids.

    Science.gov (United States)

    Ordonez, Heather; Shuman, Stewart

    2013-05-17

    We are interested in the distinctive roster of helicases of Mycobacterium, a genus of the phylum Actinobacteria that includes the human pathogen Mycobacterium tuberculosis and its avirulent relative Mycobacterium smegmatis. Here, we identify and characterize M. smegmatis Lhr as the exemplar of a novel clade of superfamily II helicases, by virtue of its biochemical specificities and signature domain organization. Lhr is a 1507-amino acid monomeric nucleic acid-dependent ATPase that uses the energy of ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single strand DNA and to unwind duplexes en route. The ATPase is more active in the presence of calcium than magnesium. ATP hydrolysis is triggered by either single strand DNA or single strand RNA, yet the apparent affinity for a DNA activator is 11-fold higher than for an RNA strand of identical size and nucleobase sequence. Lhr is 8-fold better at unwinding an RNA:DNA hybrid than it is at displacing a DNA:DNA duplex of identical nucleobase sequence. The truncated derivative Lhr-(1-856) is an autonomous ATPase, 3'-to-5' translocase, and RNA:DNA helicase. Lhr-(1-856) is 100-fold better RNA:DNA helicase than DNA:DNA helicase. Lhr homologs are found in bacteria representing eight different phyla, being especially prevalent in Actinobacteria (including M. tuberculosis) and Proteobacteria (including Escherichia coli).

  9. Motif III in superfamily 2 "helicases" helps convert the binding energy of ATP into a high-affinity RNA binding site in the yeast DEAD-box protein Ded1.

    Science.gov (United States)

    Banroques, Josette; Doère, Monique; Dreyfus, Marc; Linder, Patrick; Tanner, N Kyle

    2010-03-05

    Motif III in the putative helicases of superfamily 2 is highly conserved in both its sequence and its structural context. It typically consists of the sequence alcohol-alanine-alcohol (S/T-A-S/T). Historically, it was thought to link ATPase activity with a "helicase" strand displacement activity that disrupts RNA or DNA duplexes. DEAD-box proteins constitute the largest family of superfamily 2; they are RNA-dependent ATPases and ATP-dependent RNA binding proteins that, in some cases, are able to disrupt short RNA duplexes. We made mutations of motif III (S-A-T) in the yeast DEAD-box protein Ded1 and analyzed in vivo phenotypes and in vitro properties. Moreover, we made a tertiary model of Ded1 based on the solved structure of Vasa. We used Ded1 because it has relatively high ATPase and RNA binding activities; it is able to displace moderately stable duplexes at a large excess of substrate. We find that the alanine and the threonine in the second and third positions of motif III are more important than the serine, but that mutations of all three residues have strong phenotypes. We purified the wild-type and various mutants expressed in Escherichia coli. We found that motif III mutations affect the RNA-dependent hydrolysis of ATP (k(cat)), but not the affinity for ATP (K(m)). Moreover, mutations alter and reduce the affinity for single-stranded RNA and subsequently reduce the ability to disrupt duplexes. We obtained intragenic suppressors of the S-A-C mutant that compensate for the mutation by enhancing the affinity for ATP and RNA. We conclude that motif III and the binding energy of gamma-PO(4) of ATP are used to coordinate motifs I, II, and VI and the two RecA-like domains to create a high-affinity single-stranded RNA binding site. It also may help activate the beta,gamma-phosphoanhydride bond of ATP. (c) 2009 Elsevier Ltd. All rights reserved.

  10. Alfalfa Water Use and Yield under Different Sprinkler Irrigation Regimes in North Arid Regions of China

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    Yan Li

    2017-08-01

    Full Text Available Alfalfa (Medicago sativa is one of the major crops grown in Northern China in recent years, however, the current serious water shortage conditions present a challenge to the growth of this crop, especially if efficient use of water is considered in forage production for sustainability. This study aimed to evaluate alfalfa productivity and water use efficiency (WUE under different sprinkler irrigation levels. This experiment was conducted at Shiyanghe Experimental Station for Water-Saving in Agriculture and Ecology of China Agricultural University in Wuwei, Gansu, China, over a period of two years. There were three irrigation treatments: A1: 100% measured evapotranspiration (ETc of alfalfa; A2: irrigation amount was 66% of A1; A3: irrigation amount was 33% of A1; and a control of A4: no irrigation during the growing season. A randomized block design with three replications were applied. The results showed that the ETc and forage yield of alfalfa decreased, while WUE and crude protein (CP increased with the decreasing irrigation amounts. The seasonal average ETc and yield ranged from 412 mm to 809 mm and from 11,577 to 18,636 kg/ha, respectively, under different irrigation levels. The highest yields were obtained from the first growth period in all treatments in both years, due to the winter irrigation and the longest growth period. Alfalfa grown under lesser irrigation treatment conditions had higher variability in ETc and yield, mainly due to the variability in the amount of rainfall during the growth period. The seasonal average WUE of treatments ranged from 22.78 to 26.84 kg/(mm·ha, and the highest WUE was obtained at the first growth period, regardless of treatments. Seasonal average CP content ranged from 18.99% to 22.99%. A significant linear relationship was found between yield and ETc or irrigation amount, and the fitting results varied between growth periods and years. The present results also implied that winter irrigation provided the

  11. Interactions of alfalfa hay and sodium propionate on dairy calf performance and rumen development.

    Science.gov (United States)

    Beiranvand, H; Ghorbani, G R; Khorvash, M; Nabipour, A; Dehghan-Banadaky, M; Homayouni, A; Kargar, S

    2014-01-01

    The objective of this experiment was to investigate the effects of different levels of alfalfa hay (AH) and sodium propionate (Pro) added to starter diets of Holstein calves on growth performance, rumen fermentation characteristics, and rumen development. Forty-two male Holstein calves (40±2kg of birth weight) were used in a complete randomized design with a 3×2 factorial arrangement of treatments. Dietary treatments were as follows: (1) control = concentrate only; (2) Pro = concentrate with 5% sodium propionate [dry matter (DM) basis]; (3) 5% AH = concentrate + 5% alfalfa hay (DM basis); (4) 5% AH + Pro = concentrate + 5% alfalfa hay + 5% sodium propionate (DM basis); (5) 10% AH = concentrate + 10% alfalfa hay (DM basis); and (6) 10% AH + Pro = concentrate + 10% alfalfa hay + 5% sodium propionate (DM basis). All calves were housed in individual pens bedded with sawdust until 10wk of age. They were given ad libitum access to water and starter throughout the experiment and were fed 2L of milk twice daily. Dry matter intake was recorded daily and body weight weekly. Calves from the control, 10% AH, and 10% AH + Pro treatments were euthanized after wk 10, and rumen wall samples were collected. Feeding of forage was found to increase overall dry matter intake, average daily gain, and final weight; supplementing sodium propionate had no effect on these parameters. Calves consuming forage had lower feed efficiency than those on the Pro diet. Rumen fluid in calves consuming forage had higher pH and greater concentrations of total volatile fatty acids and molar acetate. Morphometric parameters of the rumen wall substantiated the effect of AH supplementation, as plaque formation decreased macroscopically. Overall, the interaction between forage and sodium propionate did not affect calf performance parameters measured at the end of the experiment. Furthermore, inclusion of AH in starter diets positively enhanced the growth performance of male Holstein calves and influenced

  12. Comparative analysis of alfalfa (Medicago sativa L.) leaf transcriptomes reveals genotype-specific salt tolerance mechanisms.

    Science.gov (United States)

    Lei, Yunting; Xu, Yuxing; Hettenhausen, Christian; Lu, Chengkai; Shen, Guojing; Zhang, Cuiping; Li, Jing; Song, Juan; Lin, Honghui; Wu, Jianqiang

    2018-02-15

    Soil salinity is an important factor affecting growth, development, and productivity of almost all land plants, including the forage crop alfalfa (Medicago sativa). However, little is known about how alfalfa responds and adapts to salt stress, particularly among different salt-tolerant cultivars. Among seven alfalfa cultivars, we found that Zhongmu-1 (ZM) is relatively salt-tolerant and Xingjiang Daye (XJ) is salt-sensitive. Compared to XJ, ZM showed slower growth under low-salt conditions, but exhibited stronger tolerance to salt stress. RNA-seq analysis revealed 2237 and 1125 differentially expressed genes (DEGs) between ZM and XJ in the presence and absence of salt stress, among which many genes are involved in stress-related pathways. After salt treatment, compared with the controls, the number of DEGs in XJ (19373) was about four times of that in ZM (4833). We also detected specific differential gene expression patterns: In response to salt stress, compared with XJ, ZM maintained relatively more stable expression levels of genes related to the ROS and Ca 2+ pathways, phytohormone biosynthesis, and Na + /K + transport. Notably, several salt resistance-associated genes always showed greater levels of expression in ZM than in XJ, including a transcription factor. Consistent with the suppression of plant growth resulting from salt stress, the expression of numerous photosynthesis- and growth hormone-related genes decreased more dramatically in XJ than in ZM. By contrast, the expression levels of photosynthetic genes were lower in ZM under low-salt conditions. Compared with XJ, ZM is a salt-tolerant alfalfa cultivar possessing specific regulatory mechanisms conferring exceptional salt tolerance, likely by maintaining high transcript levels of abiotic and biotic stress resistance-related genes. Our results suggest that maintaining this specific physiological status and/or plant adaptation to salt stress most likely arises by inhibition of plant growth in ZM through

  13. Oxidative stability of chicken meat during storage influenced by the feeding of alfalfa meal

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    Jana Tkáčová

    2015-05-01

    Full Text Available The aim of our experiment was to determine the effect of the alfalfa meal component in feed mixtures of Ross broiler chickens on oxidative stability of meat. Proportion of alfalfa meal in feed mixtures was 4 and 6%. The results were compared to the control group without alfalfa meal in feed mixtures. At the end of the experiment (day 38, 6 pcs of broiler chickens from each group with an average live body weight over 1 800 g were randomly selected. The samples for chemical analysis consisted of identical proportion of breast and thigh muscle, and about 1 cm2 of skin with subcutaneous fat. Fat from the meat was obtained after the samples drying. A fat was determined by extraction by means of laboratory instrument Det N Gras Selecta P. The oxidative stability of meat on the basis of acid number of fat was determided by chemical analysis. Chicken meat was stored at -18 °C for 12 months and 18 months. The acid number of fat of stored meat for 12 months was 7.38 mg KOH per g in the control group, 7.42 mg KOH per g in the group with a proportion of 4% alfalfa meal, and 11.18 mg KOH per g in the group with proportion 6% alfalfa meal. An acid number of fat of stored meat for 18 months was 5.90 mg KOH per g in the control group, 4.65 mg KOH per g in the group with a proportion of 4% alfalfa meal, and 7.07 mg KOH per g in the group with a proportion of 6% alfalfa meal. Chicken meat is notably sensitive to lipid oxidation because of its high content of polyunsaturated fatty acids. Legislation in Title 5 of Part 3 of the Codex Alimentarius of the Slovak Republic and the Government Regulation No. 286/2003 Coll. in the Annex 4 in Part B provide the requirements for animal fats and meat products. Regulation of the European Parliament and Council (EC No. 853/2004 lays down specific hygiene rules for food of animal origin. In particular, determination of free fatty acids content of rendered animal fat (tallow, lard, other animal fat. Legislative regulation does

  14. Weaned beef calves fed selenium-biofortified alfalfa hay have an enriched nasal microbiota compared with healthy controls

    Science.gov (United States)

    Hall, Jean A.; Isaiah, Anitha; Estill, Charles T.; Pirelli, Gene J.; Suchodolski, Jan S.

    2017-01-01

    Selenium (Se) is an essential trace mineral important for immune function and overall health of cattle. The nasopharyngeal microbiota in cattle plays an important role in overall respiratory health, especially when stresses associated with weaning, transport, and adaptation to a feedlot affect the normal respiratory defenses. Recent evidence suggests that cattle diagnosed with bovine respiratory disease complex have significantly less bacterial diversity. The objective of this study was to determine whether feeding weaned beef calves Se-enriched alfalfa (Medicago sativa) hay for 9 weeks in a preconditioning program prior to entering the feedlot alters nasal microbiota. Recently weaned beef calves (n = 45) were blocked by sex and body weight, randomly assigned to 3 treatment groups with 3 pens of 5 calves per treatment group, and fed an alfalfa hay based diet for 9 weeks. Alfalfa hay was harvested from fields fertilized with sodium selenate at a rate of 0, 45.0 or 89.9 g Se/ha. Blood samples were collected biweekly and analyzed for whole-blood Se concentrations. Nasal swabs were collected during week 9 from one or two calves from each pen (total n = 16). Calculated Se intake from dietary sources was 3.0, 15.6, and 32.2 mg Se/head/day for calves consuming alfalfa hay with Se concentrations of 0.34 to 2.42 and 5.17 mg Se/kg dry matter, respectively. Whole-blood Se concentrations after 8 weeks of feeding Se-fertilized alfalfa hay were dependent upon Se-application rates (0, 45.0, or 89.9 g Se/ha) and were 155, 345, and 504 ng/mL (PLinear calves fed selenium-biofortified alfalfa hay compared with control calves showed that Se-supplementation tended to be associated with an enriched nasal microbiota. ANOSIM of unweighted UniFrac distances showed that calves fed high Se-biofortified alfalfa hay clustered separately when compared with control calves in the PCoA plot (R = 0.216, P = 0.04). The bacterial orders Lactobacillales and Flavobacteriales were increased in healthy

  15. Nanomechanical microcantilever operated in vibration modes with use of RNA aptamer as receptor molecules for label-free detection of HCV helicase.

    Science.gov (United States)

    Hwang, Kyo Seon; Lee, Sang-Myung; Eom, Kilho; Lee, Jeong Hoon; Lee, Yoon-Sik; Park, Jung Ho; Yoon, Dae Sung; Kim, Tae Song

    2007-11-30

    We report the nanomechanical microcantilevers operated in vibration modes (oscillation) with use of RNA aptamers as receptor molecules for label-free detection of hepatitis C virus (HCV) helicase. The nanomechanical detection principle is that the ligand-receptor binding on the microcantilever surface induces the dynamic response change of microcantilevers. We implemented the label-free detection of HCV helicase in the low concentration as much as 100 pg/ml from measuring the dynamic response change of microcantilevers. Moreover, from the recent studies showing that the ligand-receptor binding generates the surface stress on the microcantilever, we estimate the surface stress, on the oscillating microcantilevers, induced by ligand-receptor binding, i.e. binding between HCV helicase and RNA aptamer. In this article, it is suggested that the oscillating microcantilevers with use of RNA aptamers as receptor molecules may enable one to implement the sensitive label-free detection of very small amount of small-scale proteins.

  16. Identification of molecular markers associated with Verticillium wilt resistance in alfalfa (Medicago sativa L.) using high-resolution melting.

    Science.gov (United States)

    Zhang, Tiejun; Yu, Long-Xi; McCord, Per; Miller, David; Bhamidimarri, Suresh; Johnson, David; Monteros, Maria J; Ho, Julie; Reisen, Peter; Samac, Deborah A

    2014-01-01

    Verticillium wilt, caused by the soilborne fungus, Verticillium alfalfae, is one of the most serious diseases of alfalfa (Medicago sativa L.) worldwide. To identify loci associated with resistance to Verticillium wilt, a bulk segregant analysis was conducted in susceptible or resistant pools constructed from 13 synthetic alfalfa populations, followed by association mapping in two F1 populations consisted of 352 individuals. Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were used for genotyping. Phenotyping was done by manual inoculation of the pathogen to replicated cloned plants of each individual and disease severity was scored using a standard scale. Marker-trait association was analyzed by TASSEL. Seventeen SNP markers significantly associated with Verticillium wilt resistance were identified and they were located on chromosomes 1, 2, 4, 7 and 8. SNP markers identified on chromosomes 2, 4 and 7 co-locate with regions of Verticillium wilt resistance loci reported in M. truncatula. Additional markers identified on chromosomes 1 and 8 located the regions where no Verticillium resistance locus has been reported. This study highlights the value of SNP genotyping by high resolution melting to identify the disease resistance loci in tetraploid alfalfa. With further validation, the markers identified in this study could be used for improving resistance to Verticillium wilt in alfalfa breeding programs.

  17. Effect of absorbed dose and storage length on electron paramagnetic resonance (EPR) signal strength in irradiated alfalfa seeds

    International Nuclear Information System (INIS)

    Li Naining

    2006-01-01

    A kind of alfalfa seeds was irradiated by 1, 2, 3, 4 and 5 kGy at a dose rate of 6.288 kGy·h -1 in a self-shielded irradiator of 137 Cs gamma rays. The EPR spectra, which were measured subsequently between 0.3401 and 0.3501 T, showed that there was a direct proportional relationship between the EPR signal strength of free radicals produced by gamma irradiation in the alfalfa seeds and absorbed dose. The first derivative EPR spectra of the alfalfa seeds were very clear and easy to identify. However, the EPR signal strength of the peak-to-peak amplitude decreased rapidly and most of them decayed beyond 50% within 3 days after the seeds were irradiated. It tended to stabilize after half a month since the seeds were irradiated. the differences of the EPR signal strength between the irradiated and unirradiated alfalfa seeds still remained. All seeds were stored at ambient temperature for more than 3 months. Therefore, using EPR spectrometry technique to measure free radicals in alfalfa seeds as a means to determine whether the seeds have been irradiated or not is feasible, relatively fast and simple. (authors)

  18. Identification of molecular markers associated with Verticillium wilt resistance in alfalfa (Medicago sativa L. using high-resolution melting.

    Directory of Open Access Journals (Sweden)

    Tiejun Zhang

    Full Text Available Verticillium wilt, caused by the soilborne fungus, Verticillium alfalfae, is one of the most serious diseases of alfalfa (Medicago sativa L. worldwide. To identify loci associated with resistance to Verticillium wilt, a bulk segregant analysis was conducted in susceptible or resistant pools constructed from 13 synthetic alfalfa populations, followed by association mapping in two F1 populations consisted of 352 individuals. Simple sequence repeat (SSR and single nucleotide polymorphism (SNP markers were used for genotyping. Phenotyping was done by manual inoculation of the pathogen to replicated cloned plants of each individual and disease severity was scored using a standard scale. Marker-trait association was analyzed by TASSEL. Seventeen SNP markers significantly associated with Verticillium wilt resistance were identified and they were located on chromosomes 1, 2, 4, 7 and 8. SNP markers identified on chromosomes 2, 4 and 7 co-locate with regions of Verticillium wilt resistance loci reported in M. truncatula. Additional markers identified on chromosomes 1 and 8 located the regions where no Verticillium resistance locus has been reported. This study highlights the value of SNP genotyping by high resolution melting to identify the disease resistance loci in tetraploid alfalfa. With further validation, the markers identified in this study could be used for improving resistance to Verticillium wilt in alfalfa breeding programs.

  19. Effect of increasing the level of alfalfa hay in finishing beef heifer diets on intake, sorting, and feeding behavior.

    Science.gov (United States)

    Madruga, A; González, L A; Mainau, E; Ruíz de la Torre, J L; Rodríguez-Prado, M; Manteca, X; Ferret, A

    2018-02-15

    Eight rumen cannulated Simmental heifers (BW = 281.4 ± 7.28 kg) were randomly assigned to one of four experimental treatments in a 4 × 4 replicated Latin square design to ascertain the effects of increasing levels of alfalfa hay on intake, sorting, and feeding behavior in comparison to barley straw as forage source. Treatments tested were four total mixed rations with: 1) 10% barley straw (10BS) with 7.0% NDF from forage, 2) 13% alfalfa hay (13AH) and less NDF from forage (5.7%) than 10BS, 3) 16% alfalfa hay (16AH) and the same NDF from forage (7.0%) as 10BS, and 4) 19% alfalfa hay (19AH) and more NDF from forage (8.3%) than 10BS. Each experimental period consisted of 3 wk for adaptation and 1 wk for sampling. Increasing the proportion of alfalfa hay in the diet linearly increased (P comparison to the 10BS diet. In the same way, intake of long, medium, and short particle size was greater in this diet. Moreover, heifers fed 19AH sorted for medium particle size and tended to sort for long and short particles size, and against fine particle size. Sorting behavior and meal length increased in the 19AH diet, which leads us to think that sorting feed ingredients requires time and therefore lengthens the meal. Time spent ruminating was greater in heifers fed 19AH, thus reducing the risk of ruminal acidosis when animals are fed high concentrate diets.

  20. Mycobacterium tuberculosis DinG is a structure-specific helicase that unwinds G4 DNA: implications for targeting G4 DNA as a novel therapeutic approach.

    Science.gov (United States)

    Thakur, Roshan Singh; Desingu, Ambika; Basavaraju, Shivakumar; Subramanya, Shreelakshmi; Rao, Desirazu N; Nagaraju, Ganesh

    2014-09-05

    The significance of G-quadruplexes and the helicases that resolve G4 structures in prokaryotes is poorly understood. The Mycobacterium tuberculosis genome is GC-rich and contains >10,000 sequences that have the potential to form G4 structures. In Escherichia coli, RecQ helicase unwinds G4 structures. However, RecQ is absent in M. tuberculosis, and the helicase that participates in G4 resolution in M. tuberculosis is obscure. Here, we show that M. tuberculosis DinG (MtDinG) exhibits high affinity for ssDNA and ssDNA translocation with a 5' → 3' polarity. Interestingly, MtDinG unwinds overhangs, flap structures, and forked duplexes but fails to unwind linear duplex DNA. Our data with DNase I footprinting provide mechanistic insights and suggest that MtDinG is a 5' → 3' polarity helicase. Notably, in contrast to E. coli DinG, MtDinG catalyzes unwinding of replication fork and Holliday junction structures. Strikingly, we find that MtDinG resolves intermolecular G4 structures. These data suggest that MtDinG is a multifunctional structure-specific helicase that unwinds model structures of DNA replication, repair, and recombination as well as G4 structures. We finally demonstrate that promoter sequences of M. tuberculosis PE_PGRS2, mce1R, and moeB1 genes contain G4 structures, implying that G4 structures may regulate gene expression in M. tuberculosis. We discuss these data and implicate targeting G4 structures and DinG helicase in M. tuberculosis could be a novel therapeutic strategy for culminating the infection with this pathogen. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.