Figure 1 - uploaded by Arqam Alomari
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1. Brief Summary of the Fixing of Single Nicked DNA. This figure shows the formation of phosphodiester bond at single-strand DNA substrate breaks between adjacent 3′-hydroxyl and 5′-phosphate via using LigA protein and NAD + as essential cofactor.
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DNA ligases are essential enzymes into two pathways in the cell: replication process and repair the breaks in DNA that occur as a result of damage. In E.coli, there are in fact two DNA ligases: LigA (already described its structure) and LigB as a second ligase (unknown its structure) that has a different DNA and protein sequence.
The overall aim of...
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Introduction:
There is compelling evidence on a robust nexus between inflammation and the risk of atherosclerotic cardiovascular disease. C-reactive protein (CRP) is a sensitive marker of systemic inflammation and its reduction is paralleled by significant improvement of cardiovascular events. Statins are known to lower CRP and this reduction has b...
Citations
... The cheA was expressed more in 15% NaCl than in the 5% NaCl conditions, which might be attributed to its role in the bacterial chemotactic system. The overexpression of ligA and ruvB, which plays an important role in DNA processes (Alomari, 2018) and recombination, respectively, was upregulated in both conditions. Nucleotide repairrelated genes in bacteria have previously been reported to be important for bacterial survival under salt stress (Mirete et al.,FIGURE 5 The differentially expressed genes (DEGs) of strain YJPS3-2 between 5% NaCl and 20% NaCl conditions. ...
Solar salterns were placed along the coast and were frequently left unattended after use. While many studies have isolated and identified microorganisms from hypersaline environments, their role and adaptation mechanisms are still unclear. Herein, we elucidated the role of halophiles in salt-polluted areas through the recently reported Halomonas getboli YJPS3-2 from the abandoned saltern. We analyzed the expression levels of genes in the YJPS3-2 strain to identify its adaptation mechanisms to high salinity environments, by representing the process from tidal flats to abandoned salterns with varying salinity gradients. The YJPS3-2 strain primarily overexpresses genes associated with ABC transport to adapt to hypersaline environments. Interestingly, the cheA gene, which recognizes changes in the surrounding, was the most upregulated, and it was also associated with the overexpression of the MS ring and T3SS mechanisms relating to the flagellar activity. The YJPS3-2 recognized the high salt concentration in its surroundings and attempted to accumulate compatible solutes that could withstand high osmotic pressure inside the cell to adapt to the high salinity environment. Furthermore, during this process, the YJPS3-2 strain removed surrounding pollutants and secreted secondary metabolites that could be utilized by neighboring organisms. Our results suggested that this halophilic bacterium has the potential to serve as a pioneering species for thriving the surrounding while adapting to saline environments.
... The prepared Enolase enzyme structure and the optimized sorbate were subject to a number of docking runs. The best binding conformation was selected based by following to "standard" docking solutions considered as typical in docking analysis i.e., (1) the minimal binding energy, that reflects the best docking pose, (2) the lowest with lowest root mean square deviation (RMSD) value that validate the docking process (Angelova et al., 2017), (Alomari, 2018). ...
For the first time, a density functional theory (DFT) study was conducted on the structure of a well-known antibacterial agent namely potassium 2,4-Hexadienoate, in order to elucidate its vibrational, electronic and reactivity proprieties. Structure optimization was performed using three common hybrid functionals (DFT/ B3LYP-D3; DFT/ M05-2X and DFT/M06-2X) to identify the suitable functional. Geometric parameters, IR and UV-vis spectra were well reproduced when using DFT/M06-2X with 6-311(d)G+ basis set (R2 = 0.99913). The assimilation of IR frequencies has been achieved using potential energy distribution (PED)analysis at M06-2X/6-311(d) G + level. Time-dependent density functional theory (TD-DFT) and natural bond orbital (NBO) analysis were realized to identify the excited states of 2,4-Hexadienoate anion in the liquid phase, using the solute electron density solvation model (SMD). Moreover, reactive sites in the molecule were localized by molecular electrostatic potential (MEP) analysis. Highest Occupied Molecular Orbitals (HOMO), lowest Unoccupied Molecular Orbitals (LUMO) and energy gap (HOMO-LUMO gap), were used to calculate global reactivity descriptors (GRDs), according to the frontier molecular orbitals (FMO) theory, the resulting values were analyzed to explore the chemical reactivity of the molecule and elucidate the structure-activity relationship.
... Then last step heat cycle at 72°C for 1.5 minutes to complete the elongation of the starter. After done all PCR process, the DNA fragments determine by electrophoresis at 120 voltage,50 minutes and 400 mv, within 1% agarose gel (Albanna, 2017 andAlomari, 2017). ...
Abstract
Although the idea of micro–organism such as bacteria in standard is dangerous to humans, A quantity of its
species are taken into consideration to be of superb cost and safety, especially in organic therapy, including
the institution Bacteria Probiotics. Lactobacillus salivarius is one of the maximum fundamental forms of
bacteria which can be innocent to people and which may also play a main position in their bioremediation
potential in general. Moreover, Lactobacillus salivarius was identified by traditional methods using MRS
agar selective medium, then by biochemical methods using the VITEK 2 method. Finally, Lactobacillus
salivarius was confirmed using Multi Sequencing (MLST) and Biofilm technique. The main objective of
this research is to isolate and characterize the novel bacterium salivarius Lacto from Greek yogurt and their
ability for biological assay and for study to determine the effect of bacteriocin, which is secreted by these
bacteria, and to study the extent to which these by-products to reduce environmental pollution by removing
heavy metals from various environmental media by these products.
... Two µl of ELPS from E. coli were used for electrophoresis in 2% agarose containing ethidium bromide for detection of any DNA and/or RNA contaminants. However, the sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was used according to (27)(28)(29) to determine the purity of the product from protein residues and the detection of the molecular weight of LPS. The SDS-PAGE gel was stained with both instant Blue TM (expedeon, UK) for detection of protein (26,(29)(30)(31) and sensitive silver stain (26,(31)(32)(33)(34) to visualized both protein contamination and the lipopolysaccharide. ...
... However, the sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was used according to (27)(28)(29) to determine the purity of the product from protein residues and the detection of the molecular weight of LPS. The SDS-PAGE gel was stained with both instant Blue TM (expedeon, UK) for detection of protein (26,(29)(30)(31) and sensitive silver stain (26,(31)(32)(33)(34) to visualized both protein contamination and the lipopolysaccharide. ...
In this study, we tried to extract and purify the LPS from E. coli local isolate and determine the molecular weight, purity, and pyrogenic effect of the product and compare it with standard E. coli O55:B5 LPS, the E. coli LPS was extracted by using hot phenol method then SDS-PAGE was used with both Coomassie blue and silver nitrate stain to determine its molecular weight and protein contamination also we used HPLC to the estimation of E. coli LPS purity and finally the pyrogenicity of extracted E. coli LPS was tested by using rabbit pyrogen test. The result showed that the hot phenol method with enzymatic treatment gave highly pure LPS with a high yield reach up to 242.4 mg, staining the SDS page gel with Coomassie blue and silver nitrate uncover the high purification of the extracted LPS (ELPS) with no protein contamination, with a molecular weight range between 15-23 kDa, HPLC test reveals that purity of ELPS was 100 % compared with standard LPS. The rabbits' pyrogen test confirmed that the biological activity of ELPS. In conclusion, the LPS was extracted with high purity compare with standard LPS and without any protein or DNA contamination by using the hot phenol method also the extracted rough LPS was slightly lighter than the standard LPS used but this did not affect its biological activity which remained intact.
... The obtained results in this paper from the investigation the effect of Mg +2 ion on Staphylococcus aureus-DNA Ligases enzyme type A (SLE-A) activity showed that 500 µM of Mg +2 ion had the best on ligases's activity for fixing the nick in the DNA between the 20 mer and 30 mer, and transfer them to 50 mer. Comparing this result with different study by using ammonium sulphate ion to determine how much this ion affected to the E. coli DNA Ligase activity (LigA), and the result was showed that the best concentration of ammonium sulphate was as well 500 µM, which is indicated the similarity between these ions activity on different enzymes (26) . Moreover, the results can be concluded that DNA ligases of E. coli and Staphylococcus aureus are structurally similar. ...
Ligases enzymes were discovered as a member of the nucleotidyl transferase family. Here in this paper, DNA Ligase is extracted from S. aureus works with the cofactor NAD + to make a phosphodiester bond and reform between the 3'hydroxyl and 5'phosphate DNA end. Staphylococcus aureus-DNA Ligases Enzyme type A (SLE-A) contains two essential domains; NTase and OB-fold domain, which are the most essential domains for the enzyme function. The main aim of the study is to investigate the activity of SLE-A in the presence of magnesium ion (Mg +2) by evaluating several kinetic parameters on a time course. The result showed that SLE-A has optimal activity at 500 µM of Mg +2. Furthermore, the low number of Equilibrium Association Constant (K m value) explains the binding affinity between DNA ligase of Staphylococcus aureus SLE-A enzyme and Mg +2 ion was very high and sold.
In mammalian cells, the key of ligases for DNA replication was represented to DNA ligase enzyme type 1. It is considered as a vital enzyme and required in recombination and repair processes. Also, the Human DNA ligase enzyme type 1 is essential for encodes as a part of the family of ATP-dependent ligase. According to requirements for ligases function, they are classified into two groups; one group uses ATP such as Eukaryotes and the other needs NAD + such as bacteria. The main work in the current study is to clone, express and purify Human-DNA Ligase Enzyme type 1 gene (H-Lig1). The H-Lig1 gene consists of an open reading frame containing 2760 bp, which encoded for 919 amino acids residues. This gene was synthesized into an empty plasmid by GeneArt (Life Technologies, Fisher Scientific/UK) and sent as double-stranded DNA with individual plasmid. The key objective of cloning and purification of H-Lig1 is to demonstrate the effect of G-418 Disulfate on Human Lig1 protein activity in vitro, since DNA ligase of prokaryotic cells observe no similarity to the eukaryote ligases. Here in this study it is found that the activity of H-Lig1 protein (represented to Human-DNA Ligase 1) in vitro was not inhibited by using G-418 Disulfate and did not show any inhibition and the half-maximal inhibition concentration of G-418 [IC50] was N/A, which is indicating the prospective DNA ligases as novel antibiotic targets against ligase of bacteria. The results have referred that in spite of DNA ligase in prokaryotes and eukaryotes are functionally similar. However, they are structurally different.
