Groove

Distribution by Scientific Domains
Distribution within Life Sciences

Kinds of Groove

  • deep groove
  • hydrophobic groove
  • minor groove
  • nuclear groove
  • peptide-binding groove

  • Terms modified by Groove

  • groove binder

  • Selected Abstracts


    Influence of , -Alanine on Hairpin Polyamide Orientation in the DNA Minor Groove

    HELVETICA CHIMICA ACTA, Issue 6 2003
    Victor
    Antiparallel polyamides containing 1H -pyrrole, 1H -imidazole, and 3-hydroxy-1H -pyrrole amino acids display a preference for minor-groove binding oriented NC with respect to the 5,-3, direction of the DNA helix. We find that replacement of a central Py/Py pair with a ,/, pair within a ten-ring hairpin relaxes the orientation preference and, for some DNA sequences, causes the polyamide to prefer the opposite CN orientation. Substitution of the achiral , -aminobutanoic acid (,) with either (R)(or S)-2-(acetylamino)-4-aminobutanoic acid moderates the orientation preference of the 2- , -2-hairpin. [source]


    E-improvisation: collaborative groupware technology expands the reach and effectiveness of organizational improvisation

    KNOWLEDGE AND PROCESS MANAGEMENT: THE JOURNAL OF CORPORATE TRANSFORMATION, Issue 4 2002
    Brent McKnight
    With today's increasing pace of change, managers who are struggling to continuously adapt and survive are turning to an emerging management technique known as organizational improvisation. This field of management science draws from a metaphor based in improvisational theatre and jazz music and is defined as: The ability to spontaneously recombine knowledge, processes and structure in real time, resulting in creative problem solving that is grounded in the realities of the moment. As part of these changes, organizations are working across great distances and in groups that include diverse constituents such as suppliers, partners and customers. The distance separating these team members poses a problem for improvisation as improvisation relies heavily on interpersonal communication between group members. The collaborative wealth of creativity, innovation and productivity flows in part from this real-time interaction. The increasing distance between group members hampers the effective reach of organizational improvisation. The proposed concept of e-improvisation suggests that the adoption of groupware collaborative software, in particular a peer-to-peer offering called Groove, can extend the reach of improvisation and enhance its effectiveness. Copyright © 2002 John Wiley & Sons, Ltd. [source]


    Ultrastructure of the Harmful Unarmored Dinoflagellate Cochlodinium polykrikoides (Dinophyceae) with Reference to the Apical Groove and Flagellar Apparatus

    THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 4 2010
    MITSUNORI IWATAKI
    ABSTRACT. The external and internal ultrastructure of the harmful unarmored dinoflagellate Cochlodinium polykrikoides Margalef has been examined with special reference to the apical groove and three-dimensional structure of the flagellar apparatus. The apical groove is U-shaped and connected to the anterior sulcal extension on the dorsal side of the epicone. The eyespot is located dorsally and composed of two layers of globules situated within the chloroplast. A narrow invagination of the plasma membrane is associated with the eyespot. The nuclear envelope has normal nuclear pores similar to other eukaryotes but different from the Gymnodinium group with diagnostic nuclear chambers. The longitudinal and transverse basal bodies are separated by approximately 0.5,1.0 ,m and interconnected directly by a striated basal body connective and indirectly by microtubular and fibrous structures. Characteristic features of the flagellar apparatus are as follows: (1) a nuclear extension projects to the R1 (longitudinal microtubular root) and is connected to the root by thin fibrous material; (2) fibrillar structures are associated with the longitudinal and transverse flagellar canal; and (3) a striated ventral connective extends toward the posterior end of the cell along the longitudinal flagellar canal. We conclude, based on both morphological and molecular evidence, that Cochlodinium is only distantly related to Gymnodinium. [source]


    Effect of Auxiliary Grooves on Molar Crown Preparations Lacking Resistance Form: A Laboratory Study

    JOURNAL OF PROSTHODONTICS, Issue 2 2008
    DClinDent, GradDipClinDent, Po-Ching Lu BDSc(Hons)
    Abstract Purpose: To investigate the effect of auxiliary grooves on resistance to dislodgment of crowns on compromised molar preparations lacking resistance form. Materials and Methods: Thirty human molar teeth were randomly assigned to three groups of ten, and prepared to a height-to-width ratio of 0.3 with a total convergence of 50°, and 1-mm shoulder margin. Base metal alloy copings were constructed with a 45° loading platform and cemented with zinc phosphate cement under a 50 N load. Initially, resistance testing was conducted using a Universal Testing Machine (Instron) at 1 mm/min for all 30 specimens. Following crown dislodgment, Group 1 copings were recemented and retested, Group 2 had one axial groove added, and Group 3 had two axial grooves added. New copings for Groups 2 and 3 were made, cemented, and again tested for resistance. Standardized radiographs were taken prior to initial cementation and scanned into digital images. The percentage of area occupied by the pulpal chamber above the acrylic mounting (PS), and the closest distance to pulp from the preparation surface (CD) were measured. Results: Recementation or the addition of one groove did not affect the dislodgment values (p > 0.05), but addition of two grooves caused a highly significant increase in resistance (p < 0.001). Regression analysis showed an inverse relationship between initial resistance values and pulpal space area. Lower resistance values were observed when the pulpal space area was large (p= 0.004). Conclusions: Crowns can be recemented without affecting resistance to dislodgment. Two grooves should be incorporated into compromised molar crown preparations to increase resistance form. Teeth with large pulps and therefore less coronal dentine have poorer resistance form, and therefore would benefit from placement of auxiliary grooves. [source]


    Activity-induced dental modification in holocene siberian hunter-fisher-gatherers

    AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 2 2010
    Andrea Waters-Rist
    Abstract The use of teeth as tools provides clues to past subsistence patterns and cultural practices. Five Holocene period hunter-fisher-gatherer mortuary sites from the south-western region of Lake Baikal, Siberia, Russian Federation, are observed for activity-induced dental modification (AIDM) to further characterize their adaptive regimes. Grooves on the occlusal surfaces of teeth are observed in 25 out of 123 individuals (20.3%) and were most likely produced during the processing of fibers from plants and animals, for making items such as nets and cordage. Regional variation in the frequency of individuals with occlusal grooves is found in riverine versus lakeshore sites. This variation suggests that production of material culture items differed, perhaps in relation to different fishing practices. There is also variation in the distribution of grooves by sex: grooves are found predominately in females, except at the Late Neolithic-Bronze Age river site of Ust'-Ida I where grooves are found exclusively in males. Occlusal grooves were cast using polyvinylsiloxane and maxillary canine impressions were examined by scanning electron microscopy (SEM) to determine striation patterns. Variation in striae orientation suggests that a variety of activities, and/or different manufacturing techniques, were involved in groove production. Overall, the variability in occlusal groove frequency, sex and regional distribution, and microscopic striae patterns, points to the multiplicity of activities and ways in which people used their mouths and teeth in cultural activities. Am J Phys Anthropol 143:266,278, 2010. © 2010 Wiley-Liss, Inc. [source]


    RNA Grooves Can Accommodate Disulfide-Bridged Bundles of ,-Helical Peptides

    CHEMBIOCHEM, Issue 6 2010
    Soonsil Hyun Dr.
    Feelin' groovy: A strategy for chemical stapling increases structural as well as chemical stability of helical peptides. Using an amphiphilic peptide with Leu/Lys, two Leu residues were replaced by Cys. Helical bundle peptides were generated by oxidative disulfide bond formation. One of these has a Kd as low as 21 pM against hairpin targets. This observation demonstrates that the groove in small hairpin RNA has sufficient room to contain a helical bundle peptide. [source]


    Recurrent Ingrown Big Toenails Are Efficiently Treated by CO2 Laser

    DERMATOLOGIC SURGERY, Issue 6 2002
    Francis Serour MD
    background. Surgery for onychocryptosis has a high rate of recurrence. objective. To evaluate CO2 laser partial matricectomy for recurrent onychocryptosis. methods. One hundred ninety-six consecutive patients (predominantly teenagers) previously unsuccessfully treated by surgery underwent CO2 laser for recurrent onychocryptosis. After a digital nerve block and a simple partial nail plate avulsion, the laser was used (5 W, defocused 2 mm beam in continuous mode) to vaporize the matrix, the lateral horn, and the lateral nail groove, including local granulation tissue if present. Follow-up was at least 12 months. results. Three hundred forty-four matricectomies were performed. Disease was mostly at stage II and III, with severe local infection in 24 cases (12.2%). All wounds healed in 21.9 ± 3.2 days, with no postoperative local infection or prolonged exudative drainage. Onychocryptosis reoccurred in 5 of 344 treated margins (1.45%, average 15 months), all after primary bilateral matricectomy. Spicules in the lateral nail groove occurred in 14 of 344 treated margins (4%, average 5.9 months), mostly after primary bilateral matricectomy (7 cases) and in infected margins (8 cases). One patient developed a neuroma in the lateral nail groove. conclusion. CO2 laser is effective for the treatment of recurrent onychocryptosis. Bilateral matricectomy and local infection seem to be the predisposing factors for recurrence and postoperative spicule growth. [source]


    Sensillary morphology on the rostral apex and their possible role in prey location behaviour of the carnivorous stinkbug, Eocanthecona furcellata (Wolff) (Heteroptera: Pentatomidae)

    ACTA ZOOLOGICA, Issue 3 2009
    Pathipati Usha Rani
    Abstract Eocanthecona furcellata (Wolff), the carnivorous heteropteran, demonstrates interesting feeding mechanisms that suggest the involvement of the antennal and labial tip sensilla. This study was conducted to identify the morphology of various sensilla present on the labial tip of this insect using scanning electron microscopy. Four morphologically different types of trichoid sensilla comprise the largest and most numerous sensilla and occur throughout the surface of the labial tip. Three new and unique types of sensilla were discovered. Long hairs with profusely branched shafts are present at the entrance of the rostral groove. An oval-shaped peg surrounded by sensory hairs with branched shafts and a short, stout peg encircled by a group of long hair-like sensilla was found among the sensilla population of two lobes. The morphology of the new sensilla is given and possible functions of individual receptors are suggested on morphological grounds. [source]


    Genital system anatomy and development of Ovatella myosotis by three-dimensional computer visualization

    ACTA ZOOLOGICA, Issue 2 2009
    Bernhard Ruthensteiner
    Abstract Adult anatomy as well as organogenesis of the genital system of the ellobiid pulmonate Ovatella myosotis is investigated in detail by means of serial sectioning and three-dimensional computer reconstruction and visualization. From the middle portion of the adult, which has four nidamental glands, a spermoviduct leads to a common genital aperture. From here two separate structures, the vas deferens and a groove on the body surface, lead anteriorly. The latter is termed the egg groove because it carries the egg ribbon anteriorly, a function that is recognized here for the first time in the Ellobiidae. The evolution of this structure is discussed. In development, the organ system arises from four separate anlagen: (1) the ovotestis anlage, (2) the pallial anlage giving rise to the hermaphrodite duct, fertilization pouch,spermatheca complex, nidamental glandular complex and spermoviduct, (3) the bursa copulatrix anlage and (4) the anlage of the copulatory organ, vas deferens and egg groove. This development mode strongly resembles that of the siphonariid Williamia radiata, supporting its interpretation as a plesiomorphy in Pulmonata. Similarities in development of primitive pulmonates and evolution in gastropods lead to the assumption that ontogenesis of this organ system reflects evolution to some degree. [source]


    Ultrastructural study of the jaw structures in two species of Ampharetidae (Annelida: Polychaeta)

    ACTA ZOOLOGICA, Issue 3 2004
    Alexander B. Tzetlin
    Abstract Two species of jaw bearing Ampharetidae (Adercodon pleijeli (Mackie 1994) and Ampharete sp. B) were investigated in order to describe the microanatomy of the mouth parts and especially jaws of these enigmatic polychaetes. The animals of both studied species have 14,18 mouth tentacles that are about 30 µm in diameter each. In both species, the ventral pharyngeal organ is well developed and situated on the ventral side of the buccal cavity. It is composed of a ventral muscle bulb and investing muscles. The bulb consists of posterior and anterior parts separated by a deep median transversal groove. In both species, the triangular teeth or denticles are arranged in a single transversal row on the surface of the posterior part of the ventral bulb just in front of its posterior edge. There are 36 denticles in Adercodon pleijeli and 50 in Ampharete sp. B. The height of the denticles (6,12 µm) is similar in both species. Each tooth is composed of two main layers. The outer one (dental) is the electron-dense sclerotized layer that covers the tooth. The inner one consists of long microvilli with a collagen matrix between them. The thickness of the dental layer ranges from 0.95 to 0.6 µm. The jaws of the studied worms may play a certain role in scraping off microfouling. The fine structure of the jaws in Ampharetidae is very similar to that of the mandibles of Dorvilleidae, the mandibles and the maxillae of Lumbrineridae, Eunicidae and Onuphidae, and the jaws of other Aciculata. This type of jaw is characterized by unlimited growth and the absence of replacement. The occurrence of jaws in a few smaller Ampharetidae is considered as an apomorphic state. [source]


    Minireview: On the homology of the protocoel in Cephalochordata and ,lower' Deuterostomia

    ACTA ZOOLOGICA, Issue 1 2002
    Thomas Stach
    Abstract Hypotheses regarding the homology of the protocoel in planktonic deuterostome larvae and mesodermal structures in ontogenetic stages of cephalochordates are evaluated. The prevalent ,classical' hypothesis describes the protocoel as being homologous with the diverticula of Hatschek, which, on the left side, develop into the preoral pit, subsequently into Hatschek's pit and groove (in part). This hypothesis is based mainly on the position of Hatschek's diverticula anterior to the rest of the mesoderm during their enterocoelic origin. It is shown here that during development the mesodermal segment that develops into Hatschek's nephridium is the most anterior one prior to formation of Hatschek's diverticula, and this segment assumes an anteriormost position after differentiation of Hatschek's diverticula. Additional similarities between this segment and protocoels are: (i) presence of endomesodermal cells with podocytic extensions, (ii) excretory function, (iii) relatively early ontogenetic origin, (iv) probable lack of association with nervous structures, (v) probable ectodermal origin of a portion of the canal, and (vi) position relative to the mouth opening. Therefore, homology between the protocoel and the segment that becomes Hatschek's nephridium is proposed. It is concluded that a glandular structure homologous to the diverticula of Hatschek and anterior to the protocoel/Hatschek's nephridium is a synapomorphy of notochordates or chordates. [source]


    The impact of HLA-B micropolymorphism outside primary peptide anchor pockets on the CTL response to CMV

    EUROPEAN JOURNAL OF IMMUNOLOGY, Issue 4 2007
    Jacqueline
    Abstract The factors controlling epitope selection in the T cell response to persistent viruses are not fully understood, and we have examined this issue in the context of four HLA-B*35-binding peptides from the pp65 antigen of human cytomegalovirus, two of which are previously undescribed. Striking differences in the hierarchy of immunodominance between these four epitopes were observed in healthy virus carriers expressing HLA-B*3501 versus B*3508, two HLA-B allotypes that differ by a single amino acid at position 156 (HLA-B*3501, 156Leucine; HLA-B*3508, 156Arginine) that projects from the ,2 helix into the centre of the peptide-binding groove. While HLA-B*3501+ individuals responded most strongly to the 123IPSINVHHY131 and 366HPTFTSQY373 epitopes, HLA-B*3508+ individuals responded preferentially to 103CPSQEPMSIYVY114 and 188FPTKDVAL195. By comparing peptide-MHC association and disassociation rates with peptide immunogenicity, it was clear that dissociation rates correlate more closely with the hierarchy of immunodominance among the four pp65 peptides. These findings demonstrate that MHC micropolymorphism at positions outside the primary anchor residue binding pockets can have a major impact on determinant selection in antiviral T cell responses. Such influences may provide the evolutionary pressure that maintains closely related MHC molecules in diverse human populations. [source]


    XNA, (xylo Nucleic Acid): A Summary and New Derivatives

    EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 11 2005
    B. Ravindra Babu
    Abstract Fully modified homopyrimidine 2'-deoxy- xylo nucleic acid (dXNA) form triple helixes with complementary DNA/RNA with thermal stabilities comparable to those of the corresponding DNA:DNA and DNA:RNA duplexes. However, a single or few insertions of dXNA monomers in a DNA strand significantly lower duplex stabilities. The dXNA monomers are known to adopt predominantly an N -type furanose conformation in solution. With a desire to increase the binding affinity, seven sugar-modified XNA monomers (H, F, N, M, K, P and Q) have been synthesised and their effect on hybridization towards DNA and RNA complements studied. The introduction of 2'-fluoro and 2'-hydroxy substituents was expected to induce conformational restriction towards C3'- endo -type furanose conformation of monomer F derived from 1-(2'-deoxy-2'-fluoro-,- D -xylofuranosyl)thymine and monomer H derived from 1-(,- D -xylofuranosyl)thymine. The presence of functionalites facing the minor groove as in 1-(2'-amino-2'-deoxy-2'- N,4'- C -methylene-,- D -xylofuranosyl)thymine (monomer N), 1-[4- C -(N -methylpiperazinyl)methyl-,- D -xylofuranosyl]thymine (monomer P), 1-(4- C -piperazinylmethyl-,- D -xylofuranosyl)thymine (monomer Q), 1-(4- C -hydroxymethyl-,- D -xylofuranosyl)thymine (monomer M) and 9-(4- C -hydroxymethyl-,- D -xylofuranosyl)adenine (monomer K) was studied, with monomer N being locked in an N -type furanose conformation. Besides, an efficient synthesis of known xylo -LNA phosphoramidite 19, required for the incorporation of 1-(2'- O,4'- C -methylene-,- D -xylofuranosyl)thymine (monomer L) is described. For comparison, hydridization data of various XNAs reported in the literature are included in the discussion section. The thermal denaturation studies show that XNAs containing conformationally locked monomers (N and L) display improved binding affinity, and that partially modified DNA/XNA chimera, or fully modified XNA display preferential hybridization towards RNA complements. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source]


    Six major steps in animal evolution: are we derived sponge larvae?

    EVOLUTION AND DEVELOPMENT, Issue 2 2008
    Claus Nielsen
    SUMMARY A review of the old and new literature on animal morphology/embryology and molecular studies has led me to the following scenario for the early evolution of the metazoans. The metazoan ancestor, "choanoblastaea," was a pelagic sphere consisting of choanocytes. The evolution of multicellularity enabled division of labor between cells, and an "advanced choanoblastaea" consisted of choanocytes and nonfeeding cells. Polarity became established, and an adult, sessile stage developed. Choanocytes of the upper side became arranged in a groove with the cilia pumping water along the groove. Cells overarched the groove so that a choanocyte chamber was formed, establishing the body plan of an adult sponge; the pelagic larval stage was retained but became lecithotrophic. The sponges radiated into monophyletic Silicea, Calcarea, and Homoscleromorpha. Homoscleromorph larvae show cell layers resembling true, sealed epithelia. A homoscleromorph-like larva developed an archenteron, and the sealed epithelium made extracellular digestion possible in this isolated space. This larva became sexually mature, and the adult sponge-stage was abandoned in an extreme progenesis. This eumetazoan ancestor, "gastraea," corresponds to Haeckel's gastraea. Trichoplax represents this stage, but with the blastopore spread out so that the endoderm has become the underside of the creeping animal. Another lineage developed a nervous system; this "neurogastraea" is the ancestor of the Neuralia. Cnidarians have retained this organization, whereas the Triploblastica (Ctenophora+Bilateria), have developed the mesoderm. The bilaterians developed bilaterality in a primitive form in the Acoelomorpha and in an advanced form with tubular gut and long Hox cluster in the Eubilateria (Protostomia+Deuterostomia). It is indicated that the major evolutionary steps are the result of suites of existing genes becoming co-opted into new networks that specify new structures. The evolution of the eumetazoan ancestor from a progenetic homoscleromorph larva implies that we, as well as all the other eumetazoans, are derived sponge larvae. [source]


    Crack-healing behaviour and resultant high-temperature fatigue strength of machined Si3N4/SiC composite ceramic

    FATIGUE & FRACTURE OF ENGINEERING MATERIALS AND STRUCTURES, Issue 1 2008
    Y.-S. JUNG
    ABSTRACT The crack-healing behaviour of machining cracks in Si3N4/20 wt% SiC composite was investigated. The machining cracks were introduced by a heavy machining process, during the creation of a semicircular groove. The machined specimens were healed at various temperatures and times in air. The optimized crack-healing condition of the machined specimens was found to be a temperature of 1673 K and a time of 10 h. The specimens healed by this condition exhibited almost the same strength as the smooth specimens healed. Moreover, the bending strengths and the fatigue limits of the machined specimens healed were systematically investigated at temperatures from room temperature to 1673 K. The machined specimens healed at the optimized condition exhibited an almost constant bending strength (,700 MPa) up to 1673 K. Also, the specimens exhibited considerably high cyclic and static fatigue limits at temperatures from 1073 to 1573 K. These results demonstrated that the crack-healing could be an effective method for improving the structural integrity and reducing machining costs of the Si3N4/SiC composite ceramic. [source]


    Strength recovery of machined Al2O3/SiC composite ceramics by crack healing

    FATIGUE & FRACTURE OF ENGINEERING MATERIALS AND STRUCTURES, Issue 12 2007
    M. ONO
    ABSTRACT Alumina is used in various fields as a machine component. However, it has a low fracture toughness, which is a weakness. Thus, countless cracks may be initiated randomly by machining, and these cracks decrease the component's mechanical properties and reliability. To overcome this problem, a crack-healing ability could be a very useful technology. In this study, Al2O3/SiC composite was sintered. This alumina exhibits excellent crack-healing ability. Small specimens for a bending test were made from the Al2O3/SiC. A semicircular groove was machined using a diamond ball-drill. The machining reduced the local fracture stress from approximately 820,300 MPa. The machined specimens were crack-healed under various conditions. The fracture stress of these specimens after crack healing was evaluated systematically from room temperature (RT) to 1573 K. It was found that the local fracture stress of the machined specimen recovered almost completely after crack healing. Therefore, it was concluded that crack healing could be an effective method for improving the structural integrity of machined alumina and reducing machining costs. [source]


    Deformation analysis of notched components and assessment of approximate methods

    FATIGUE & FRACTURE OF ENGINEERING MATERIALS AND STRUCTURES, Issue 11 2001
    Y. Jiang
    Finite element modelling was conducted on notched members subjected to proportional and non-proportional loading. A recently developed cyclic plasticity model capable of accurately describing cyclic material behaviour was implemented into a finite element code. A plate with a central hole and a shaft with a circumference groove were studied. Approximate methods for the notched problems were critically evaluated using the finite element results. [source]


    Crystal structure and enzymatic properties of a bacterial family 19 chitinase reveal differences from plant enzymes

    FEBS JOURNAL, Issue 21 2006
    Ingunn A. Hoell
    We describe the cloning, overexpression, purification, characterization and crystal structure of chitinase G, a single-domain family 19 chitinase from the Gram-positive bacterium Streptomyces coelicolor A3(2). Although chitinase G was not capable of releasing 4-methylumbelliferyl from artificial chitooligosaccharide substrates, it was capable of degrading longer chitooligosaccharides at rates similar to those observed for other chitinases. The enzyme was also capable of degrading a colored colloidal chitin substrate (carboxymethyl-chitin,remazol,brilliant violet) and a small, presumably amorphous, subfraction of ,-chitin and ,-chitin, but was not capable of degrading crystalline chitin completely. The crystal structures of chitinase G and a related Streptomyces chitinase, chitinase C [Kezuka Y, Ohishi M, Itoh Y, Watanabe J, Mitsutomi M, Watanabe T & Nonaka T (2006) J Mol Biol358, 472,484], showed that these bacterial family 19 chitinases lack several loops that extend the substrate-binding grooves in family 19 chitinases from plants. In accordance with these structural features, detailed analysis of the degradation of chitooligosaccharides by chitinase G showed that the enzyme has only four subsites (, 2 to +,2), as opposed to six (, 3 to +,3) for plant enzymes. The most prominent structural difference leading to reduced size of the substrate-binding groove is the deletion of a 13-residue loop between the two putatively catalytic glutamates. The importance of these two residues for catalysis was confirmed by a site-directed mutagenesis study. [source]


    Site-directed mutagenesis and footprinting analysis of the interaction of the sunflower KNOX protein HAKN1 with DNA

    FEBS JOURNAL, Issue 1 2005
    Mariana F. Tioni
    The interaction of the homeodomain of the sunflower KNOX protein HAKN1 with DNA was studied by site-directed mutagenesis, hydroxyl radical footprinting and missing nucleoside experiments. Binding of HAKN1 to different oligonucleotides indicated that HAKN1 prefers the sequence TGACA (TGTCA), with changes within the GAC core more profoundly affecting the interaction. Footprinting and missing nucleoside experiments using hydroxyl radical cleavage of DNA showed that HAKN1 interacts with a 6-bp region of the strand carrying the GAC core, covering the core and nucleotides towards the 3, end. On the other strand, protection was observed along an 8-bp region, comprising two additional nucleotides complementary to those preceding the core. Changes in the residue present at position 50 produced proteins with different specificities. An I50S mutant showed a preference for TGACT, while the presence of lysine shifted the preference to TGACC, suggesting that residue 50 interacts with nucleotide(s) 3, to GAC. Mutation of Lys54,Val produced a protein with reduced affinity and relaxed specificity, able to recognize the sequence TGAAA, while the conservative change of Arg55,Lys completely abolished binding to DNA. Based on these results, we propose a model for the interaction of HAKN1 with DNA in which helix III of the homeodomain accommodates along the major groove with Arg55, Asn51, Lys54 and Ile50, establishing specific contacts with bases of the GACA sequence or their complements. This model can be extended to other KNOX proteins given the conservation of these amino acids in all members of the family. [source]


    A model of a gp120 V3 peptide in complex with an HIV-neutralizing antibody based on NMR and mutant cycle-derived constraints

    FEBS JOURNAL, Issue 3 2000
    Anat Zvi
    The 0.5, monoclonal antibody is a very potent strain-specific HIV-neutralizing antibody raised against gp120, the envelope glycoprotein of HIV-1. This antibody recognizes the V3 loop of gp120, which is a major neutralizing determinant of the virus. The antibody,peptide interactions, involving aromatic and negatively charged residues of the antibody 0.5,, were studied by NMR and double-mutant cycles. A deuterated V3 peptide and a Fab containing deuterated aromatic amino acids were used to assign these interactions to specific V3 residues and to the amino acid type and specific chain of the antibody by NOE difference spectroscopy. Electrostatic interactions between negatively charged residues of the antibody Fv and peptide residues were studied by mutagenesis of both antibody and peptide residues and double-mutant cycles. Several interactions could be assigned unambiguously: F96(L) of the antibody interacts with Pro13 of the peptide, H52(H) interacts with Ile7, Ile9 and Gln10 and D56(H) interacts with Arg11. The interactions of the light-chain tyrosines with Pro13 and Gly14 could be assigned to either Y30a(L) and Y32(L), respectively, or Y32(L) and Y49(L), respectively. Three heavy-chain tyrosines interact with Ile7, Ile20 and Phe17. Several combinations of assignments involving Y32(H), Y53(H), Y96(H) and Y100a(H) may satisfy the NMR and mutagenesis constraints, and therefore at this stage the interactions of the heavy-chain tyrosines were not taken into account. The unambiguous assignments [F96(L), H52(H) and D56(H)] and the two possible assignments of the light-chain tyrosines were used to dock the peptide into the antibody-combining site. The peptide converges to a unique position within the binding site, with the RGPG loop pointing into the center of the groove formed by the antibody complementary determining regions while retaining the ,-hairpin conformation and the type-VI RGPG turn [Tugarinov, V., Zvi, A., Levy, R. & Anglister, J. (1999) Nat. Struct. Biol.6, 331,335]. [source]


    Oligodeoxynucleotide Duplexes Containing (5,S)-5,- C -Alkyl-Modified 2,-Deoxynucleosides: Can an Alkyl Zipper across the DNA Minor-Groove Enhance Duplex Stability?

    HELVETICA CHIMICA ACTA, Issue 11 2003
    Huldreich Trafelet
    A series of oligonucleotides containing (5,S)-5,- C -butyl- and (5,S)-5,- C -isopentyl-substituted 2,-deoxyribonucleosides were designed, prepared, and characterized with the intention to explore alkyl-zipper formation between opposing alkyl chains across the minor groove of oligonucleotide duplexes as a means to modulate DNA-duplex stability. From four possible arrangements of the alkyl groups that differ in the density of packing of the alkyl chains across the minor groove, three (duplex types I,III, Fig.,2) could experimentally be realized and their duplex-forming properties analyzed by UV-melting curves, CD spectroscopy, and isothermal titration calorimetry (ITC), as well as by molecular modeling. The results show that all arrangements of alkyl residues within the minor groove of DNA are thermally destabilizing by 1.5,3°/modification in Tm. We found that, within the proposed duplexes with more loosely packed alkyl groups (type- III duplexes), accommodation of alkyl residues without extended distorsion of the helical parameters of B-DNA is possible but does not lead to higher thermodynamic stability. The more densely packed and more unevenly distributed arrangement (type- II duplexes) seems to suffer from ecliptic positioning of opposite alkyl groups, which might account for a systematic negative contribution to stability due to steric interactions. The decreased stability in the type- III duplexes described here may be due either to missing hydrophobic interactions of the alkyl groups (not bulky enough to make close contacts), or to an overcompensation of favorable alkyl-zipper formation presumably by loss of structured H2O in the minor groove. [source]


    MHC Class II epitope predictive algorithms

    IMMUNOLOGY, Issue 3 2010
    Morten Nielsen
    Summary Major histocompatibility complex class II (MHC-II) molecules sample peptides from the extracellular space, allowing the immune system to detect the presence of foreign microbes from this compartment. To be able to predict the immune response to given pathogens, a number of methods have been developed to predict peptide,MHC binding. However, few methods other than the pioneering TEPITOPE/ProPred method have been developed for MHC-II. Despite recent progress in method development, the predictive performance for MHC-II remains significantly lower than what can be obtained for MHC-I. One reason for this is that the MHC-II molecule is open at both ends allowing binding of peptides extending out of the groove. The binding core of MHC-II-bound peptides is therefore not known a priori and the binding motif is hence not readily discernible. Recent progress has been obtained by including the flanking residues in the predictions. All attempts to make ab initio predictions based on protein structure have failed to reach predictive performances similar to those that can be obtained by data-driven methods. Thousands of different MHC-II alleles exist in humans. Recently developed pan-specific methods have been able to make reasonably accurate predictions for alleles that were not included in the training data. These methods can be used to define supertypes (clusters) of MHC-II alleles where alleles within each supertype have similar binding specificities. Furthermore, the pan-specific methods have been used to make a graphical atlas such as the MHCMotifviewer, which allows for visual comparison of specificities of different alleles. [source]


    Pathogen evasion strategies for the major histocompatibility complex class I assembly pathway

    IMMUNOLOGY, Issue 1 2008
    Antony N. Antoniou
    Summary Major histocompatibility complex (MHC) class I molecules bind and present short antigenic peptides from endogenously or exogenously derived sources to CD8+ cytotoxic T lymphocytes (CTL), with recognition of a foreign peptide normally targeting the cell for lysis. It is generally thought that the high level of MHC polymorphism, which is concentrated mostly within the peptide-binding groove, is driven by the ,evolutionary arms race' against pathogens. Many pathogens have developed novel and intriguing mechanisms for evading the continuous sampling of the intracellular and intercellular environments by MHC molecules, none more so than viruses. The characterization of immunoevasion mechanisms has improved our understanding of MHC biology. This review will highlight our current understanding of the MHC class I biosynthetic pathway and how it has been exploited by pathogens, especially viruses, to potentially evade CTL recognition. [source]


    Glycolipid targets of CD1-mediated T-cell responses

    IMMUNOLOGY, Issue 3 2001
    D. Branch Moody
    Summary Members of the CD1 family of antigen-presenting molecules bind and present a variety of mammalian and microbial glycolipids for specific recognition by T cells. CD1 proteins accomplish their antigen-presenting function by binding the alkyl chains of the antigens within a deep, hydrophobic groove on the membrane distal surface of CD1, making the hydrophilic elements of the antigen available for contact with the variable regions of antigen-specific T-cell receptors. Most models of CD1-restricted T cells function in infectious, neoplastic, or autoimmune diseases and are based on the premise that CD1-restricted T-cell responses are initiated by alterations in cellular glycolipid content. Although a growing number of self, altered self and foreign glycolipid antigens have been identified, the cellular mechanisms that could lead to the generation of antigenic glycolipids within cells, or control the presentation of particular classes of altered self or microbial glycolipids in disease states have only recently come under investigation. Here we review the structures of known glycolipid antigens for T cells and discuss how the chemical nature of these antigens, which is quite different from that of peptides, influences their recognition by T cells. [source]


    Halloween genes and nuclear receptors in ecdysteroid biosynthesis and signalling in the pea aphid

    INSECT MOLECULAR BIOLOGY, Issue 2010
    O. Christiaens
    Abstract The pea aphid (Acyrthosiphon pisum) is the first whole genome sequenced insect with a hemimetabolic development and an emerging model organism for studies in ecology, evolution and development. The insect steroid moulting hormone 20-hydroxyecdysone (20E) controls and coordinates development in insects, especially the moulting/metamorphosis process. We, therefore present here a comprehensive characterization of the Halloween genes phantom, disembodied, shadow, shade, spook and spookiest, coding for the P450 enzymes that control the biosynthesis of 20E. Regarding the presence of nuclear receptors in the pea aphid genome, we found 19 genes, representing all of the seven known subfamilies. The annotation and phylogenetic analysis revealed a strong conservation in the class of Insecta. But compared with other sequenced insect genomes, three orthologues are missing in the Acyrthosiphon genome, namely HR96, PNR-like and Knirps. We also cloned the EcR, Usp, E75 and HR3. Finally, 3D-modelling of the ligand-binding domain of Ap-EcR exhibited the typical canonical structural scaffold with 12 ,-helices associated with a short hairpin of two antiparallel ,-strands. Upon docking, 20E was located in the hormone-binding groove, supporting the hypothesis that EcR has a role in 20E signalling. [source]


    The effectiveness of syringe irrigation and ultrasonics to remove debris from simulated irregularities within prepared root canal walls

    INTERNATIONAL ENDODONTIC JOURNAL, Issue 10 2004
    S.-J. Lee
    Abstract Aim, To compare the ability of syringe irrigation and ultrasonic irrigation to remove artificially placed dentine debris from simulated canal irregularities within prepared root canals. Methodology, After canal enlargement, twelve canines were split longitudinally into two halves. On the wall of one half of each root canal a standard groove of 4 mm in length, 0.2 mm in width and 0.5 mm in depth was cut, 2,6 mm from the apex, to simulate uninstrumented canal extensions. On the wall of the other half, three standard saucer-shaped depressions of 0.3 mm in diameter and 0.5 mm in depth were cut at 2, 4 and 6 mm from the apex to simulate uninstrumented canal irregularities. Each groove and depression were filled with dentine debris mixed with 2% NaOCl to simulate a situation when dentine debris accumulates in uninstrumented canal extensions and irregularities during canal preparation. Each tooth was re-assembled by reconnecting the two halves, using wire and an impression putty material. Two per cent NaOCl was then delivered into each canal either using syringe irrigation (n = 8) or using ultrasonic irrigation (n = 8). Before and after irrigation, images of the two halves of the canal wall were taken, using a microscope and a digital camera, after which they were scanned into a PC as TIFF images. The amount of remaining dentine debris in the grooves and depressions was evaluated by using a scoring system between 0,3: the higher the score, the more the debris. The data were analysed by means of the Mann,Whitney U -test. Results, Both forms of irrigation reduced the debris score significantly. The debris score was statistically significantly lower after ultrasonic irrigation than after syringe irrigation (P = 0.002 for grooves, P = 0.047 for depressions). Conclusion, Ultrasonic irrigation ex vivo is more effective than syringe irrigation in removing artificially created dentine debris placed in simulated uninstrumented extensions and irregularities in straight, wide root canals. [source]


    Endodontic and periodontal treatments of a geminated mandibular first premolar

    INTERNATIONAL ENDODONTIC JOURNAL, Issue 2 2002
    S. Aryanpour
    Abstract Aim, To describe a rare case of gemination involving a mandibular first premolar. Summary The complex morphology of geminated teeth renders their endodontic and periodontal management difficult. Root canal and periodontal treatments were performed on a geminated mandibular first premolar with three canals. Clinical examination showed two separated crowns with united roots. Radiographically, two distinct pulp chambers with two joined and a third independent canal were seen. Conventional root canal treatment resulted in complete healing of the apical lesion. However, the occurrence of a vertical fracture led to the extraction of the mesial segment. At the follow-up visit, the distal segment was clinically healthy and continued to satisfy functional demands. Key learning points ,Failure to diagnose the initial crack along a gemination groove resulted in further propagation and finally complete vertical fracture. ,Owing to the abnormal morphology of the crown and the complexity of the root canal system in geminated teeth, treatment protocols require special attention. ,For asymptomatic cases without aesthetic or orthodontic problems and without associated pathosis, routine review and careful maintenance are required. [source]


    3D tangentially injected swirling recirculating flow in a nozzle with a slotted-tube,Effects of groove parameters

    INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, Issue 11 2010
    Hui-Fen Guo
    Abstract A numerical prediction for 3D swirling recirculating flow in an air-jet spinning nozzle with a slotted-tube is carried out with the realizable k,, turbulence model. The effects of the groove parameters on the flow and yarn properties are investigated. The simulation results show that some factors, such as reverse flow upstream of the injector, vortex breakdown downstream of the injector, corner recirculation zone (CRZ) behind the step and vortex ring in the groove caused by the groove geometric variation, are significantly related to fluid flow, and consequently to yarn properties. With increasing groove height, the length of the CRZ increases, while the initial vortex ring in the groove decreases and a same direction rotating vortex forms in the bottom of the groove. Similarly, as the groove width increases, the extent of both vortex breakdown in downstream of the injectors and the vortex ring in the groove increases slightly, whereas the CRZ lengths in stream-wise direction decrease. Some factors, such as the negative tangential velocities, the size of the vortex rings in the grooves and the CRZ, are constant for nozzles with different groove lengths. Copyright © 2009 John Wiley & Sons, Ltd. [source]


    Congenital absence of the patella in an Anglo-Saxon skeleton

    INTERNATIONAL JOURNAL OF OSTEOARCHAEOLOGY, Issue 3 2003
    P. Patrick
    Abstract A skeleton of a young Anglo-Saxon woman aged about 25 years at the time of death is described. The distal femoral articulation was in two distinct parts separated by a deep groove in which the tendon of quadriceps femoris would have lain. The medial condyle of the femur was smaller than normal and there was no patellar surface on the anterior part of the articulation. The woman was of normal stature (1.53 ± 0.04 m) and no other abnormalities were found in the skeleton. It was considered that these findings were consistent with a diagnosis of congenital absence of the patella. This is the earliest recorded case of this condition. Copyright © 2003 John Wiley & Sons, Ltd. [source]


    Tunica albuginea urethroplasty for anterior urethral strictures: A urethroscopic analysis

    INTERNATIONAL JOURNAL OF UROLOGY, Issue 9 2009
    Raj K Mathur
    Objective: To assess the efficacy of tunica albuginea urethroplasty (TAU) for anterior urethral strictures. Methods: We assessed 206 patients with anterior urethral strictures who underwent TAU. The procedure involves mobilization of strictured urethra and laying it open with a dorsal slit. Edges of the slit-open urethra are sutured to edges of the urethral groove with a silicon catheter in situ. Thus in neourethra, the roof is formed by tunica albuginea of the urethral groove. Results were assessed at 6, 12, 24 and 36 months by comparative analysis of patient satisfaction along with retrograde urethrogram, urethrosonogram, uroflowmetry, and were categorized as good, fair and poor. Good and fair results were considered as successful. Thirty patients were taken for postoperative urethroscopic analysis to allow better understanding of both successful and failed cases. Results: Postoperative evaluation at 6 months showed a 96.6% success rate, which decreased to 94.7% at 1 year, 93.2% at 2 years and over 90% at the end of 3 years. The overall failure rate was 9.2%, which required revision surgery. Urethroscopic visualization of the reconstruction site showed wide, patent and distensible neourethra uniformly lined by urothelium over roof formed by tunica albuginea of the corpora cavernosa in successful cases. Failure cases showed diffuse fibrotic narrowing or circumferential scarring. Conclusion: Tunica albuginea is a locally available distensible tissue, sufficient to maintain the patency of the neourethra, without any graft or flap. TAU is easier and useful when patients have unhealthy oral mucosa due to tobacco chewing. [source]