Structural and Functional Studies of gpX of Escherichia coli Phage P2 Reveal a Widespread Role for LysM Domains in the Baseplates of Contractile-Tailed Phages

A variety of bacterial pathogenicity determinants, including the type VI secretion system and the virulence cassettes from Photorhabdus and Serratia, share an evolutionary origin with contractile-tailed myophages. The well-characterized Escherichia coli phage P2 provides an excellent system for studies related to these systems, as its protein composition appears to represent the “minimal” myophage tail. In this study, we used nuclear magnetic resonance (NMR) spectroscopy to determine the solution structure of gpX, a 68-residue tail baseplate protein. Although the sequence and structure of gpX are similar to those of LysM domains, which are a large family associated with peptidoglycan binding, we did not detect a peptidoglycan-binding activity for gpX. However, bioinformatic analysis revealed that half of all myophages, including all that possess phage T4-like baseplates, encode a tail protein with a LysM-like domain, emphasizing a widespread role for this domain in baseplate function. While phage P2 gpX comprises only a single LysM domain, many myophages display LysM domain fusions with other tail proteins, such as the DNA circulation protein found in Mu-like phages and gp53 of T4-like phages. Electron microscopy of P2 phage particles with an incorporated gpX-maltose binding protein fusion revealed that gpX is located at the top of the baseplate, near the junction of the baseplate and tail tube. gpW, the orthologue of phage T4 gp25, was also found to localize to this region. A general colocalization of LysM-like domains and gpW homologues in diverse phages is supported by our bioinformatic analysis.     

PDADMAC as a flocculant for lignosulfonate of NSSC pulping process

The spent liquor (SL) of neutral sulfite semi‐chemical (NSSC) pulping process contains about 8 wt% lignocelluloses that can be extracted and used in the production of value‐added materials. In this work, a flocculation process followed by centrifugation was considered for isolating lignosulfonate and hemicelluloses from SL. It was observed that, by adding 20 mg/g of polydiallyldimethylammuniom chloride (PDADMAC) with 100,000–200,000 g/mol molecular weight to SL, 45% of lignosulfonate and 39% of hemicelluloses were removed at 30°C. The lignocellulose removal was more efficient for the dual flocculation system of low and high molecular weights PDADMAC than for individual PDADMAC systems. Overall, 49% of lignosulfonate, 47% of hemicelluloses and 97% of turbidity were removed from SL from the dual system when 10 mg/g low molecular weight PDADMAC and 10 mg/g high molecular weight PDADMAC were added to the SL at 30°C, subsequently. The thermogravimetric analysis (TGA) of generated flocs showed that all samples had similar thermal behaviour and 13–16 wt% of flocs remained as ash after burning at 700°C in nitrogen. As the flocs are made of lignocellulosic materials and they are thermally stable, they could be used as fillers in paper board production. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:686–691, 2016     

Pyrone and pyridone compounds in the liquid culture of Physisporinus sanguinolentus

Chromatographic separation of the liquid culture filtrate of the basidiomycete fungus Physisporinus sanguinolentus has yielded three new compounds viz., 2-methyl-4-pyrone, 2-methyl-5,6-dihydro-4-pyrone and the pyridone form of 4-hydroxy-2-methylpyridine, together with the known triacetic acid lactone, the sesquiterpene dialdehyde merulidial and a derivative of merulidial. Their structures were elucidated by spectroscopic analysis and by comparison to literature data and a synthetic sample. One of the compounds, merulidial, was shown to inhibit the germination of spores and the hyphal growth of the wood-rotting basidiomycete Heterobasidion annosum and the saprophytic mould Cladosporium cucumerinum.     

DNA extraction and PCR amplification method suitable for fresh, herbarium-stored, lichenized, and other fungi

This paper presents a DNA extraction method suitable for fresh, herbarium-stored, lichenized and other fungal specimens. The method is fast and reliable, comparatively inexpensive and is suitable for obtaining PCR amplification quality DNA from large numbers of samples in a short time. The method has been tested with over 300 samples ofAscochyta, Phyllosticta, Ramalina, Parmelia andPhysconia. Amplifiable fungal DNA was extracted from pure cultures, leaf lesions, whole thalli and dissected only-fungal sections of lichenized fungi. In addition, the method has proved suitable for use with herbarium specimens of both lichenized and non-lichenized fungi, stored as dried pure cultures or dried infected plant material.     

Effect of cumulus cell removal of in vitro matured bovine oocytes prior to in vitro fertilization on subsequent cleavage rate

The aim of this study is to identify the effect of cumulus cells removal prior to the in vitro fertilization of matured bovine oocytes on cleavage rate. Denuded, matured oocytes were fertilized in presence or absence of loose cumulus cells, cumulus cell conditioned IVF medium (CCCM), charcoal-treated CCCM and charcoal-treated CCCM supplemented with progesterone at a final concentration of 150 ng/ml. After 18 h of incubation with sperm, the presumptive embryos were cultured on a BRL monolayer and the percentage of cleaved embryos was evaluated on Day 4. Removal of cumulus cells prior to IVF significantly reduced the cleavage rate (25% for denuded oocytes versus 56% for cumulus-oocyte complexes (COCs)). The addition of loose cumulus cells partially restored the effect of denudation (cleavage rate: 37% for denuded oocytes supplemented with loose cumulus cells versus 27% for denuded oocytes and 58% for COCs). CCCM also had a positive effect on the cleavage rate of oocytes denuded prior to IVF (36% for denuded oocytes fertilized in CCCM versus 14% for denuded oocytes). Treating the CCCM with charcoal resulted in complete loss of its effect on cleavage rate (18% for denuded oocytes fertilized in charcoal-treated CCCM versus 34% for denuded oocytes fertilized in CCCM). The addition of progesterone to charcoal-treated CCCM partially restored the reduction of the cleavage rate caused by charcoal treatment (27% for denuded oocytes fertilized in charcoal-treated CCCM supplemented with progesterone versus 14% for denuded oocytes fertilized in charcoal-treated CCCM and 36% for denuded oocytes fertilized in CCCM). In conclusion, removal of cumulus cells prior to IVF adversely affects the cleavage rate through loss of a factor secreted by these cells. This factor probably is progesterone.     

Production of lignosulfonate in NSSC‐based biorefinery

The spent liquor (SL) of a neutral sulfite semichemical (NSSC) pulping process contains a considerable amount of lignocelluloses and is treated in wastewater systems. The lignocelluloses, however, can be used for producing value‐added products if they are isolated from the SL. In this article, solvent treatment (mixing acetone, ethanol, or isopropyl with SL) was used as a method for isolating lignosulfonate from SL. The maximum lignosulfonate removal was obtained via mixing isopropyl alcohol with SL at the weight ratio of 20/80, room temperature, and 5.7 pH. The results also showed that the molecular weight and anionic charge density of the precipitates were in the range of 5,000–70,000 g/mol and 0.2–1.8 meq/g, respectively. Based on these results, a process was proposed for isolating lignosulfonate from SL and converting the NSSC process to an NSSC‐based biorefinery. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1508–1514, 2015     

Molecular characterization of strawberry pathogen Gnomonia fragariae and its genetic relatedness to other Gnomonia species and members of Diaporthales

Gnomonia fragariae is a poorly studied ascomycete belonging to Diaporthales. Originally G. fragariae was considered a saprophyte occurring on dead tissues of strawberry plants. Recently this fungus was found in Latvia and Sweden, and it was proven to be the cause of severe root rot and petiole blight of strawberry. Thirteen isolates of this pathogen and several other Gnomonia species occurring on rosaceous hosts were characterized by molecular analysis using nucleotide sequences of partial LSU rRNA gene and the total ITS region. The homologous regions from relevant diaporthalean taxa available in the GenBank were also included and compared with the taxa sequenced in this study. Phylogenetic analyses revealed that G. fragariae, G. rubi, and Gnomonia sp. (CBS 850.79) were genetically different from G. gnomon, the type species of the genus, and other members of Gnomoniaceae. The analyses showed that G. fragariae and Hapalocystis were genetically very closely related, forming a phylogenetic clade, which is possibly presenting a new family in the Diaporthales. Morphological comparisons of the Gnomonia species on the basis of commonly used criteria for the taxonomy of Diaporthales, so far did not reveal any evident features for the polyphyletic status of Gnomonia.     

Proline-Functionalized Graphene Oxide Nanoparticles (GO–Pro NPs) Mitigate Salt-Induced Adverse Effects on Morpho-Physiological Traits and Essential Oils Constituents in Moldavian Balm (Dracocephalum moldavica L.)

Many methodologies have been established to lessen negative impacts of salinity on plants. Of those methodologies, nanoparticles (NPs) application has achieved great importance thanks to their unique physico-chemical properties. Consequently, formerly respecting encouraging impacts of graphene oxide (GO) and proline (Pro) on different plant processes under non-stress and stress conditions, proline-functionalized graphene oxide nanoparticles “GO–Pro NPs” were synthesized and characterized. Graphite powder, as starting material, was used to synthesize GO using modified Hummers method followed by functionalization of its surface by proline in basic media. Afterward, GO–Pro NPs, GO and Pro, each at 0, 50 and 100 mg L^?1 concentrations with three replications, were applied on Moldavian balm (Dracocephalum moldavica L.) plants to assay their effects under non-stress (0 mM) and salt stress (50 and 100 mM) conditions. GO–Pro NPs and Pro effectively alleviated negative effects of salinity through increasing morphological parameters, photosynthetic pigments, chlorophyll fluorescence parameters, chlorophyll index (SPAD), and membrane stability index (MSI) and decreasing hydrogen peroxide and malondialdehyde, as well. Also application of GO–Pro NPs enhanced proline, antioxidant enzymes activities, and most dominant constituents of essential oil. The highest MSI (48.87%) and proline content (15.36 µM g^?1 FW) were observed in plant treated with GO–Pro NPs (50 mg L^?1) under 100 mM NaCl salinity stress. The GO–Pro NPs treatment at lower dose (50 mg L^?1) could be introduced as the best preservative treatment for Moldavian balm under salt stress. GO application mostly had no effect on the measured parameters announcing it as carrier for Pro to enhance its efficiency. In conclusion, GO–Pro NPs application could promote Moldavian balm performance and essential oil under salinity presenting GO–Pro NPs as new treatment against stress conditions.

     

Application of hemicelluloses precipitated via ethanol treatment of pre-hydrolysis liquor in high-yield pulp

Hemicelluloses in industrially produced pre-hydrolysis liquor (PHL) were precipitated with ethanol. These PHL-derived hemicelluloses (PHL-EH) and a commercial, pure birch wood xylan sample (powder form) (BWX) were bleached using chlorine dioxide (D(0) and D(1)) and hydrogen peroxide (Ep) in the D(0)EpD(1) sequence, and the chemical compositions, molecular weights and charge densities of the treated samples were assessed. When applied to high-yield pulp (HYP) at 50 mg/g, 26 and 20 mg/g of the bleached PHL-EH and BWX, respectively, were adsorbed without significantly affecting paper properties. These results suggest that semi-bleached hemicelluloses could be used to increase the basis weight of paper products. Furthermore, an integrated process was proposed that converts the kraft-based dissolving pulp production process into a biorefinery unit with dissolving pulp, bleached hemicelluloses and lignin as main products.