Functional equivalence of the uridine turn and the hairpin as building blocks of tertiary structure in the Neurospora VS ribozyme.

Mutational, kinetic, and chemical modification experiments show that one of the three-way helical junctions in the Neurospora VS ribozyme contains a uridine turn that is important for organizing the functional three-dimensional structure of this junction. Disruption of the uridine turn disrupts the structure of the junction and decreases the self-cleavage activity of the ribozyme; however, substitution of the uridine turn with a variety of different hairpins, thereby transforming the three-way junction into a four-way junction, maintains catalytic activity. Chemical modification structure probing reveals that both the native junction and the hairpin-containing junction support the same tertiary interactions required elsewhere in the ribozyme for catalysis. These observations show that functionally equivalent three-dimensional RNA structures can be built from different secondary structure elements.     

Probing binding mechanism of interleukin-6 and olokizumab: in silico design of potential lead antibodies for autoimmune and inflammatory diseases

Computer-aided antibody engineering has been successful in the design of new biologics for disease diagnosis and therapeutic interventions. Interleukin-6 (IL-6), a well-recognized drug target for various autoimmune and inflammatory diseases such as rheumatoid arthritis, multiple sclerosis, and psoriasis, was investigated in silico to design potential lead antibodies. Here, crystal structure of IL-6 along with monoclonal antibody olokizumab was explored to predict antigen–antibody (Ag???Ab)-interacting residues using DiscoTope, Paratome, and PyMOL. Tyr56, Tyr103 in heavy chain and Gly30, Ile31 in light chain of olokizumab were mutated with residues Ser, Thr, Tyr, Trp, and Phe. A set of 899 mutant macromolecules were designed, and binding affinity of these macromolecules to IL-6 was evaluated through Ag???Ab docking (ZDOCK, ClusPro, and Rosetta server), binding free-energy calculations using Molecular Mechanics/Poisson Boltzman Surface Area (MM/PBSA) method, and interaction energy estimation. In comparison to olokizumab, eight newly designed theoretical antibodies demonstrated better result in all assessments. Therefore, these newly designed macromolecules were proposed as potential lead antibodies to serve as a therapeutics option for IL-6-mediated diseases.     

The determination of spatial pattern inDictyostelium discoideum

Free-living amoebae of the cellular slime mouldDictyostelium discoideum aggregate when starved and give rise to a long and thin multicellular structure, the slug. The slug resembles a metazoan embryo, and as with other embryos it is possible to specify a fate map. In the case ofDictyostelium discoideum the map is especially simple: cells in the anterior fifth of the slug die and form a stalk while the majority of those in the posterior differentiate into spores. The genesis of this anterior-posterior distinction is the subject of our review. In particular, we ask: what are the relative roles of individual pre-aggregative predispositions and post-aggregative position in determining cell fate? We review the literature on the subject and conclude that both factors are important. Variations in nutritional status, or in cell cycle phase at starvation, can bias the probability that an amoeba differentiates into a stalk cell or a spore. On the other hand, isolates, or slug fragments, consisting of only prestalk cells or only prespore cells can regulate so as to result in a normal range of both cell types. We identify three levels of control, each being responsible for guiding patterning in normal development: (i) ‘coin tossing’, whereby a cell autonomously exhibits a preference for developing along either the stalk or the spore pathway with relative probabilities that can be influenced by the environment; (ii) ‘chemical kinetics’, whereby prestalk and prespore cells originate from undifferentiated amoebae on a probabilistic basis but, having originated, interact (e.g. via positive and negative feedbacks), and the interaction influences the possibility of conversion of one cell type into the other; and (iii) ‘positional information’, in which the spatial distribution of morphogens in the slug influences the pathway of differentiation. In the case of possibilities (i) and (ii), sorting out of like cell types leads to the final spatial pattern. In the case of possibility (iii), the pattern arisesin situ     

Embryology ofMalaxis saprophyta,with comments on the systematic position ofMalaxis (Orchidaceae)

InMalaxis saprophyta, anther wall development corresponds to the Monocotyledonous type. The uninucleate tapetum is of secretory type and the endothecium develops U- and V-shaped thickenings on the inner tangential and radial walls. Cytokinesis is simultaneous; tetrahedral, isobilateral and T-shaped tetrads are formed which are compactly aggregated in pollinia. At anthesis the microspore tetrads are 2-celled. The ovule is anatropous, bitegmic and both integuments are dermal in origin. A single hypodermal cell develops directly into a megaspore mother cell. Embryo sac development is predominantly monosporic and less often bisporic. Irrespective of the type of development, the mature embryo sac is 6-nucleate. Although double fertilization occurs, the primary endosperm nucleus degenerates. Embryogeny is of the Onagrad type. The mature embryo lacks differentiation into cotyledon, plumule and radicle. The reticulate seed coat is formed entirely by the outer layer of outer integument. There are three sterile and three fertile valves in the ovary. Although initially parenchymatous, the entire three sterile valves in the ovary and the upper half of the three fertile valves become sclerified after fertilization. The embryological characters support the disputed systematic position ofMalaxis within subtribeMalaxidinae ofEpidendreae.     

Metabolism of Monoterpenes : Evidence for the Function of Monoterpene Catabolism in Peppermint (Mentha piperita) Rhizomes

l-Menthone of peppermint leaves is reduced to d-neomenthol which is glucosylated and transported to the rhizome, whereupon the β-d-glucoside is hydrolyzed, the aglycone oxidized back to l-menthone, and this ketone converted to l-3,4-menthone lactone. l-[G-³H]-3,4-Menthone lactone and its labeled progenitors, when incubated with excised mint rhizomes, gave rise to nonvolatile lipids as well as polar metabolites. The lipids thus generated consisted of labeled squalene and phytosterols in the nonsaponifiable fraction and C₁₄-C₂₆ fatty acids in the saponifiable fraction. These results imply degradation of the terpenoid to acetylcoenzyme A and reduced pyridine nucleotide, and reincorporation of label via these products. Starch and soluble carbohydrates were also found to be labeled; however, chemical degradation of the [³H]glucose obtained on hydrolysis of starch indicated the presence of tritium only on interior carbons, suggesting that labeling had occurred via reduced pyridine nucleotides. Analysis of the labeled organic acids revealed the presence of several hydroxy methylacyl intermediates suggesting the operation of a modified β-oxidation pathway in the degradation of the acyclic terpenoid skeleton. The results indicate that monoterpenes transported to the rhizome are oxidized to yield acetyl-coenzyme A and reduced pyridine nucleotides, and suggest that metabolic turnover of monoterpenes in mint represents a mechanism for recycling carbon and energy from foliar terpenes into other metabolites of the rhizome.     

ABC transporters mined through comparative transcriptomics associate with organ-specific accumulation of picrosides in a medicinal herb,Picrorhiza kurroa

Protoplasma - Picrorhiza kurroa Royle ex Benth is a valuable medicinal herb of North-Western Himalayas due to presence of two major bioactive compounds, picroside-I and picroside-II used in the...     

Haemonchus contortus: The in vitro effects of dl-tetramisole and rafoxanide on glycolytic enzymes

Kaur R. and Sood M. L. 1982. Haemonchus contortus: the in vitro effects of dl-tetramisole and rafoxanide on glycolytic enzymes. International Journal for Parasitology 12: 585–588. Various enzymes of glycolysis (hexokinase, phosphoglucomutase, phosphoglucoisomerase, adolase, glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase, phosphoglyceromutase-enolase-pyruvate kinase and lactate dehydrogenase) have been detected in adult Haemonchus contortus. Low pyruvate kinase and lactate dehydrogenase activities suggested an alternate pathway from phosphoenolpyruvate. In vitro incubation had no significant effects on these enzymes and the worm was able to maintain normal metabolism for 12 h. Varying degrees of inhibition of glycolytic enzymes were observed with 50 μg/ml of dl-tetramisole and rafoxanide. The enzymes were inhibited to a greater extent by dl-tetramisole. These effects may block the glycolytic pathway and deprive the parasite of its ATP production.