Comprehensive analysis of draft genomes of two closely related pseudomonas syringae phylogroup 2b strains infecting mono- and dicotyledon host plants

Comparison of the prophage region in Pseudomonas syringae strain SM (A) with the corresponding regions in strains 1845 (B) and 2507 (C) using MAUVE software (Darling et al. 2010). (PNG 2118 kb

In Situ SERS Sensing by a Laser-Induced Aggregation of Silver Nanoparticles Templated on a Thermoresponsive Polymer

A stimuli-responsive (pH- and thermoresponsive) micelle-forming diblock copolymer, poly(1,2-butadiene) 290 - block -poly( N , N -dimethylaminoethyl methacrylate) 240 (PB- b -PDMAEMA), was used as a polymer template for the in situ synthesis of silver nanoparticles (AgNPs) through Ag + complexation with PDMAEMA blocks, followed by the reduction of the bound Ag + with sodium borohydride. A successful synthesis of the AgNPs on a PB- b -PDMAEMA micellar template was confirmed by means of UV–Vis spectroscopy and transmission electron microscopy, wherein the shape and size of the AgNPs were determined. A phase transition of the polymer matrix in the AgNPs/PB- b -PDMAEMA metallopolymer hybrids, which results from a collapse and aggregation of PDMAEMA blocks, was manifested by changes in the transmittance of their aqueous solutions as a function of temperature. A SERS reporting probe, 4-mercaptophenylboronic acid (4-MPBA), was used to demonstrate a laser-induced enhancement of the SERS signal observed under constant laser irradiation. The local heating of the AgNPs/PB- b -PDMAEMA sample in the laser spot is thought to be responsible for the triggered SERS effect, which is caused by the approaching of AgNPs and the generation of “hot spots” under a thermo-induced collapse and the aggregation of the PDMAEMA blocks of the polymer matrix. The triggered SERS effect depends on the time of a laser exposure and on the concentration of 4-MPBA. Possible mechanisms of the laser-induced heating for the AgNPs/PB- b -PDMAEMA metallopolymer hybrids are discussed

Elucidation of a masked repeating structure of the O-specific polysaccharide of the halotolerant soil bacteria Azospirillum halopraeferens Au4

Abstract An O-specific polysaccharide was obtained by mild acid hydrolysis of the lipopolysaccharide isolated by the phenol-water extraction from the halotolerant soil bacteria Azospirillum halopraeferens type strain Au4. The polysaccharide was studied by sugar and methylation analyses, selective cleavages by Smith degradation and solvolysis with trifluoroacetic acid, one-and two-dimensional 1 H and 13 C NMR spectroscopy. The following masked repeating structure of the O-specific polysaccharide was established: →3)- where non-stoichiometric substituents, an O-methyl group (~45%) and a side-chain glucose residue (~65%), are shown in italics. 63

Mu2e Technical Design Report

The Mu2e experiment at Fermilab will search for charged lepton flavor violation via the coherent conversion process mu- N --> e- N with a sensitivity approximately four orders of magnitude better than the current world's best limits for this process. The experiment's sensitivity offers discovery potential over a wide array of new physics models and probes mass scales well beyond the reach of the LHC. We describe herein the preliminary design of the proposed Mu2e experiment. This document was created in partial fulfillment of the requirements necessary to obtain DOE CD-2 approval.Comment: compressed file, 888 pages, 621 figures, 126 tables; full resolution available at http://mu2e.fnal.gov; corrected typo in background summary, Table 3.

The role of epiphytic populations in pathogenesis of the genus Xanthomonas bacteria

Global climate warming and involvement of new regions with endemic populations of microorganisms in commercial seed production have led to an increase in the diversity of phytopathogenic bacteria that are affecting major crops, including the fruit trees. As a rule, emergence of new pathogens is associated with importation of infected seeds and planting material, cultivation of new species and varieties of plants, and expansion of agricultural trade with foreign countries. One of the leaders in diversity among phytopathogens is the genus Xanthomonas bacteria, affecting more than 400 plant species. Among the characteristic signs of xanthomonads is the high frequency of horizontal gene transfer both within the genus and between phylogenetically removed bacterial taxa – up to 25% of the genes are of this origin. In this paper, we consider another source of increasing the number of phytopathogenic species – by the epiphytic populations. These bacteria are the likely ancestral form of the phytopathogenic bacteria of the genus Xanthomonas

GENETIC UNIFORMITY OF A SPECIFIC REGION IN SARS-CoV-2 GENOME AND REPURPOSING OF N-ACETYL-D-GLUCOSAMINE

The causative agent of the viral pneumonia outbreak in the world identified as SARS-CoV-2 leads to a severe respiratory illness like SARS and MERS. The pathogen spreading has turned into a pandemic dissemination and increased the mortality rate. Therefore, any useful information is essential for effective control of the disease. Our findings show the existence of unvarying sequence with no mutation in ORF1ab regions from 134 high-quality filtered genome sequences of SARS-CoV-2 downloaded from the GISAID database. We have detected this sequence region by using MAUVE analysis and pairwise alignment using Global Needleman Wunsch algorithm. All these results were also confirmed with the Clustal W analysis. The first 6500 bp of the consensus genome including ORF1ab region is an unvarying sequence in SARS-CoV-2 genome. Unvarying sequence in SARS-CoV-2 genome has been very similar to another spike protein, which belongs to feline infectious peritonitis virus strain UU4 (PDB 6JX7), depending on amino acid sequences encoded, and N-acetyl-D-glucosamine is the ligand of this protein according to the highest TM-score of predicted protein structure analysis. These results have confirmed that N-acetyl-D-glucosamine could play an important effect on pathogenicity of SARS-CoV-2. Also, our molecular docking analysis data supports a strong protein-ligand interaction of N-acetyl-D-glucosamine with spike receptor-binding domain bound with ACE2 (PDB 6M0J) and RNA-binding domain of nucleocapsid phosphoprotein (PDB 6WKP) from SARS-CoV-2. Therefore, binding of N-acetyl-D-glucosamine to these proteins could inhibit SARS-CoV-2’s replication. In the present work, we have suggested providing a repurposing compound for further in vitro and in vivo studies and new insights for ongoing clinical treatments as a new strategy to control of SARS-CoV-2 infections

Molecular dynamics analysis of N-acetyl-D-glucosamine against specific SARS-CoV-2’s pathogenicity factors

The causative agent of the pandemic identified as SARS-CoV-2 leads to a severe respiratory illness similar to SARS and MERS with fever, cough, and shortness of breath symptoms and severe cases that can often be fatal. In our study, we report our findings based on molecular docking analysis which could be the new effective way for controlling the SARSCoV-2 virus and additionally, another manipulative possibilities involving the mimicking of immune system as occurred during the bacterial cell recognition system. For this purpose, we performed molecular docking using computational biology techniques on several SARSCoV-2 proteins that are responsible for its pathogenicity against N-acetyl-D-glucosamine. A similar molecular dynamics analysis has been carried out on both SARS-CoV-2 and anti-Staphylococcus aureus neutralizing antibodies to establish the potential of N-acetyl-D-glucosamine which likely induces the immune response against the virus. The results of molecular dynamic analysis have confirmed that SARS-CoV-2 spike receptor-binding domain (PDB: 6M0J), RNA-binding domain of nucleocapsid phosphoprotein (PDB: 6WKP), refusion SARS-CoV-2 S ectodomain trimer (PDB: 6X79), and main protease 3clpro at room temperature (PDB: 7JVZ) could bind with N-acetyl-D-glucosamine that these proteins play an important role in SARS-CoV-2’s infection and evade the immune system. Moreover, our molecular docking analysis has supported a strong protein-ligand interaction of N-acetyl-Dglucosamine with these selected proteins. Furthermore, computational analysis against the D614G mutant of the virus has shown that N-acetyl-D-glucosamine affinity and its binding potential were not affected by the mutations occurring in the virus’ receptor binding domain. The analysis on the affinity of N-acetyl-D-glucosamine towards human antibodies has shown that it could potentially bind to both SARS-CoV-2 proteins and antibodies based on our predictive modelling work. Our results confirmed that N-acetyl-D-glucosamine holds the potential to inhibit several SARS-CoV-2 proteins as well as induce an immune response against the virus in the host

Development of qPCR Detection Assay for Potato Pathogen <i>Pectobacterium atrosepticum</i> Based on a Unique Target Sequence

The recent taxonomic diversification of bacterial genera Pectobacterium and Dickeya, which cause soft rot in plants, focuses attention on the need for improvement of existing methods for the detection and differentiation of these phytopathogens. This research presents a whole genome-based approach to the selection of marker sequences unique to particular species of Pectobacterium. The quantitative real-time PCR assay developed is selective in the context of all tested Pectobacterium atrosepticum strains and is able to detect fewer than 102 copies of target DNA per reaction. The presence of plant DNA extract did not affect the sensitivity of the assay