Genome annotation and comparative genomic analysis of <Emphasis Type="Italic">Bacillus subtilis</Emphasis> MJ01, a new bio-degradation strain isolated from oil-contaminated soil

One of the main challenges in elimination of oil contamination from polluted environments is improvement of biodegradation by highly efficient microorganisms. Bacillus subtilis MJ01 has been evaluated as a new resource for producing biosurfactant compounds. This bacterium, which produces surfactin, is able to enhance bio-accessibility to oil hydrocarbons in contaminated soils. The genome of B. subtilis MJ01 was sequenced and assembled by PacBio RS sequencing technology. One big contig with a length of 4,108,293 bp without any gap was assembled. Genome annotation and prediction of gene showed that MJ01 genome is very similar to B. subtilis spizizenii TU-B-10 (95% similarity). The comparison and analysis of orthologous genes carried out between B. subtilis MJ01, reference strain B. subtilis subsp. subtilis str. 168, and close relative spizizenii TU-B-10 by microscope platform and various bioinformatics tools. More than 88% of 4269 predicted coding sequences in MJ01 had at least one similar sequence in genome of reference strain and spizizenii TU-B-10. Despite this high similarity, some differences were detected among encoding sequences of non-ribosome protein and bacteriocins in MJ01 and spizizenii TU-B-10. MJ01 has unique nucleotide sequences and a novel predicted lasso-peptide bacteriocin; it also has not any similar nucleotide sequence in non-redundant nucleotide data base.     

Axonal cytoskeletal changes after non-disruptive axonal injury

In animal models of human diffuse axonal injury, axonal swellings leading to secondary axotomy occur between 2 and 6 h after injury. But, analysis of cytoskeletal changes associated with secondary axotomy has not been undertaken. We have carried out a quantitative analysis of cytoskeletal changes in a model of diffuse axonal injury 4 h after stretch-injury to adult guinea-pig optic nerves. The major site of axonal damage was the middle portion of the nerve. There was a statistically significant increase in the proportion of small axons with a diameter of 0.5 μm and smaller in which there was compaction of neurofilaments. Axons with a diameter greater than 2.0 μm demonstrated an increased spacing between cytoskeletal elements throughout the length of the nerve. However, in the middle segment of the nerve these larger axons demonstrated two different types of response. Either, where periaxonal spaces occurred, there was a reduction in axonal calibre, compaction of neurofilaments but no change in their number, and a loss of microtubules. Or, where intramyelinic spaces occurred there was an increased spacing between neurofilaments and microtubules with a significant loss in the number of both. Longitudinal sections showed foci of compaction of neurofilaments interspersed between regions where axonal structure was apparently normal. Neurofilament compaction was correlated with disruption of the axolemma at these foci present some hours after injury. We suggest that the time course of these axonal cytoskeletal changes after stretch-injury to central axons is shorter than those changes documented to occur during Wallerian degeneration.     

Multiway analysis applied to time‐resolved chemiluminescence for simultaneous determination of paracetamol and codeine in pharmaceuticals

This method is based on the enhancing effect of codeine (COD) and paracetamol (PAR) on the chemiluminescence (CL) reaction of Ru(phen)₃²⁺ with Ce(IV). In the batch mode, COD gives a relatively sharp peak with the highest CL intensity at 4.0 s, whereas the maximum CL intensity of the PAR appears at ~60 s after injection of Ce(IV) solution. Whole CL time profiles allowed use of the time‐resolved CL data in combination with multiway calibration techniques, as multiway partial least squares (N‐PLS), for the quantitative determination of both COD and PAR in binary mixtures. In this work, we found that the impact of Ce(IV) concentration on the CL intensity was different for COD and PAR. Therefore, a Ce(IV) concentration mode was added to the time and sample modes to obtain 3D data. The percent relative standard deviation (%RSD) values for 10 determinations of 1.0 × 10^?5 mol/L of COD and 1.0 × 10^?4 mol/L of PAR were 6.1% and 8.7%, respectively. The limit of detection (LOD) values (S/N = 3) were 0.9 × 10^?8 mol/L and 1.0 × 10^?6 mol/L for COD and PAR, respectively. The proposed method was successfully applied to the determination of PAR and COD in commercial pharmaceutical formulations. Acceptable recoveries (90–110%) were obtained for the quantification of these drugs in the real samples. Copyright © 2016 John Wiley & Sons, Ltd.     

Can Lionel Messi’s brain slow down time passing?

It seems that seeing others in slow-motion by heroes does not belong only to movies. When Lionel Messi plays football, you can hardly see anything from him that other players cannot do. Then why he is not stoppable really? It seems the answer may be that opponents do not have enough time to do what they want; because in Messi’s neural system, time passes slower. In differential equations that model a single neuron, this speed can be generated by multiplying an equal term in all equations. Or maybe interactions between neurons and the structure of neural networks play this role.     

Preparation of pre-cut corneas from fresh donated whole globes for Descemet’s stripping automated keratoplasty: 3-year results at the Central Eye Bank of Iran

To describe the technique and the results of the preparation of pre-cut corneas for Descemet’s stripping automated endothelial keratoplasty (DSAEK) during a 3-year period at the Central Eye Bank of Iran (CEBI). The method of preparation of pre-cut corneas from donated whole globes at the CEBI is described and the frequency and percentage of pre-cut corneas prepared for DSAEK, between April 2009 and March 2012, are specified. Moreover, post-operative reports are reviewed for any complaints about using pre-cut tissues for DSAEK. Out of the 1,518 donated whole globes appropriate for DSAEK, 1,478 (97.4 %) pre-cut corneas were successfully prepared. The method of preparation failed in 40 (2.6 %) cases. Based on the eye bank post-operative reports, thickness of pre-cut tissues for DSAEK was deemed unacceptable in only 6 (0.4 %) cases prior to surgery; five of these were too thick and one was too thin. Preparation of pre-cut corneas, for DSAEK from donated whole globes, in the CEBI is a safe and easy method, with very good preservation of endothelial cells after the preparation of the pre-cut corneas and reduced risks from corneal manipulation.     

Tyrosyl-DNA Phosphodiesterase I Catalytic Mutants Reveal an Alternative Nucleophile That Can Catalyze Substrate Cleavage

Tyrosyl-DNA phosphodiesterase I (Tdp1) catalyzes the repair of 3′-DNA adducts, such as the 3′-phosphotyrosyl linkage of DNA topoisomerase I to DNA. Tdp1 contains two conserved catalytic histidines: a nucleophilic His (His^nuc) that attacks DNA adducts to form a covalent 3′-phosphohistidyl intermediate and a general acid/base His (His^gab), which resolves the Tdp1-DNA linkage. A His^nuc to Ala mutant protein is reportedly inactive, whereas the autosomal recessive neurodegenerative disease SCAN1 has been attributed to the enhanced stability of the Tdp1-DNA intermediate induced by mutation of His^gab to Arg. However, here we report that expression of the yeast His^nucAla (H182A) mutant actually induced topoisomerase I-dependent cytotoxicity and further enhanced the cytotoxicity of Tdp1 His^gab mutants, including H432N and the SCAN1-related H432R. Moreover, the His^nucAla mutant was catalytically active in vitro, albeit at levels 85-fold less than that observed with wild type Tdp1. In contrast, the His^nucPhe mutant was catalytically inactive and suppressed His^gab mutant-induced toxicity. These data suggest that the activity of another nucleophile when His^nuc is replaced with residues containing a small side chain (Ala, Asn, and Gln), but not with a bulky side chain. Indeed, genetic, biochemical, and mass spectrometry analyses show that a highly conserved His, immediately N-terminal to His^nuc, can act as a nucleophile to catalyze the formation of a covalent Tdp1-DNA intermediate. These findings suggest that the flexibility of Tdp1 active site residues may impair the resolution of mutant Tdp1 covalent phosphohistidyl intermediates and provide the rationale for developing chemotherapeutics that stabilize the covalent Tdp1-DNA intermediate.     

Join queries optimization in the distributed databases using a hybrid multi-objective algorithm

Cluster Computing - In the distributed database systems, the relations needed by a query can be kept in several locations. This process significantly increases potential corresponding Query...     

Metronidazole aryloxy,carboxy and azole derivatives: Synthesis,anti-tumor activity,QSAR, molecular docking and dynamics studies

A series of novel metronidazole aryloxy, carboxy and azole derivatives has been synthesized and their cytotoxic activities on three cancer cell lines were evaluated by MTT assay. Compounds 4m, 4l and 4d showed the most potent cytotoxic activity (IC₅₀s?less than?100?µg/mL). Apoptosis was also detected for these compounds by flow cytometry. Docking studies were performed in order to propose the probable target protein. In the next step, molecular dynamics simulation was carried out on the proposed target protein, focal adhesion kinase (FAK, PDB code: 2ETM), bound to compound 4m. As, 4m showed a potent cytotoxic activity and an acceptable apoptotic effect, it can be a potential anticancer candidate that may work through inhibition of FAK.     

Training early visuo-spatial abilities: A controlled classroom-based intervention study

Visuo-spatial training is considered a promising approach to provide young children with a sound foundation for later mathematical learning. We developed and implemented a tablet-based visuo-spatial intervention in kindergarten classrooms aiming to foster the development of children’s visuo-spatial and numerical abilities. A sample of N?=?125 children participated in the present study, 68 children were part of the intervention group and participated in 20 training sessions of 20?min over a 10-week period, 57 children formed a business as usual control group. Results show that, at this young age, visuo-spatial and early math skills are already strongly interlinked. However, the training effects were domain-specific as they only improved visuo-spatial skills, but did not transfer to early math performance in the present setting.