Identification of potential targets in Staphylococcus aureus N315 using computer aided protein data analysis

Staphylococcus aureus is a gram positive bacterium, responsible for both community-acquired and hospital-acquired infection, resulting in a mortality rate of 39%. 43.2% resistance to methicilin and emerging resistance to Fluroquinolone and Oxazolidinone, have evoked the necessity of the establishment of alternative and effective therapeutic approach to treat this bacteria. In this computational study, various database and online software are used to determine some specific targets of Staphylococcus aureus N315 other than those used by Penicillin, Quinolone and Oxazolidinone. For this purpose, among 302 essential proteins, 101 nonhomologous proteins were accrued and 64 proteins which are unique in several metabolic pathways of S. aureus were isolated by using metabolic pathway analysis tools. Furthermore, 7 essentially unique enzymes involved in exclusive metabolic pathways were revealed by this research, which can be potential drug target. Along with these important enzymes, 15 non-homologous proteins located on membrane were identified, which can play a vital role as potential therapeutic targets for the future researchers.     

Genetic diversity assessment of Tunisian <Emphasis Type="Italic">Mycobacterium bovis</Emphasis> population isolated from cattle

Background

The genetic diversity of M. bovis in Tunisia is still underestimated despite the implementation of an eradication program. The lack of data about spatial distribution of the M. bovis population hinders the control of bovine tuberculosis (bTB) progress. This study represents the largest molecular analysis of M. bovis isolates in Tunisia. It is aimed to upgrade the understanding of bTB epidemiology and the geographical distribution of the infection. Tuberculosis research was performed in cattle (n?=?149) with TB-compatible lesions collected over 5 months from a slaughterhouse located in Sfax, Tunisia.

Results

Ninety-four animals were found to be infected by M. bovis and two others by M. caprae. Spoligotyping revealed twenty-five patterns, SB0120, SB0134, and SB0121 being the most prevalent profiles (36.4%, 11.4%, and 7.2%, respectively). Three new spoligotypes were detected: SB2345, SB2344 and SB2343. MIRU-VNTR analysis classified the isolates in seventy-three profiles and showed a large genotypic variety observed within the main spoligotype which was split into several MIRU-VNTR types: 29 in SB0120 (h?=?0.983), 10 in SB0134 (h?=?0.981) and 7 in SB0121 (h?=?1). Genotyping revealed a common pattern in different geographic regions. It also showed that Sfax, located in southern-Tunisia, represents a high-risk area with an elevated genetic diversity.

Conclusions

Spatial analysis may provide insights into disease transmission, which affects the effectiveness of eradication campaigns in cattle.

     

Role of Bacillus licheniformis in Phytoremediation of Nickel Contaminated Soil Cultivated with Rice

Heavy metal contamination in soil is an important environmental problem and it has negative effect on agriculture. Bacteria play a major role in phytoremediation of heavy metals contaminated soil. In this study, the effect of Bacillus licheniformis NCCP-59, a halophilic bacterium isolated from salt mines near Karak, Pakistan, were determined on a three week old greenhouse grown seedling and germinating seeds of two rice varieties (Basmati-385 (B-385) and KSK-282) in soil contaminated with different concentrations (0, 100, 250, 500, and 1000 ppm) of Nickel. Nickel significantly reduced the germination rate and germination percentage mainly at 500 and 1000 ppm. Significant decrease in ion contents (Na, K, and Ca) was observed while Ni ion concentration in the plant tissues increases as the concentration of Ni applied increases. The photosynthetic pigments (chlorophyll a (chl a), chlorophyll b (chl b), and carotenoids) were also decreased by the application of different concentrations of Ni. Total protein and organic nitrogen were found to be reduced at higher concentrations of Nickel. Inoculation of Bacillus Licheniformis NCCP-59 improved seed germination and biochemical attribute of the plant under Ni stress. It is clear from the results that the Bacillus Licheniformis NCCP-59 strain has the ability to protect the plants from the toxic effects of nickel and can be used for the phytoremediation of Ni contaminated soil.     

In vivo and in vitro management of Meloidogyne incognita (Tylenchida: Heteroderidae) using rhizosphere bacteria,Pseudomonas spp. and Serratia spp. compared with oxamyl

Biological control using rhizosphere bacteria, Pseudomonas spp. and Serratia spp. is a prospective alternative technique to overcome plant parasitic nematodes infection. So, the current study was conducted in vitro on five egg-masses, 100 free eggs and 100 infective juveniles (IJs) of Meloidogyne incognita as well as greenhouse treatments on Luffa aegyptiaca L. to evaluate the nematicidal potential of six strains belong to Pseudomonas spp. and Serratia spp. as compared to oxamyl.Results showed that the inhibitory effect and juvenile mortality varied according to bacteria species, strains and exposure time. All the tested bacteria significantly (P ≤ 0.05) inhibited egg hatching and increased juvenile mortality in vitro. After 3 days of treatment, Pseudomonas spp. were more effective against eggs (48.31to 55.15%) and IJs (20.98 to 25.30%) than Serratia spp. (44.55 to 49.75% with eggs) and (19.06 to 21.61% with IJs), respectively. In the pot experiment, Luffa aegyptiaca L. treated with Serratia spp. and Pseudomonas spp. displayed significantly higher (P ≤ 0.05) levels of growth (as indicated by root length, fresh roots weight and fresh shoots weight) compared to control plants and significantly (P ≤ 0.05) suppressed galling (number of galls) and reproduction (as indicated by number of egg-masses on roots and number of eggs and juveniles in pot soil). Meanwhile, among the treated plants, Serratia spp. and Pseudomonas spp. gave the best results in shoot weight of pots infected by eggs of M. incognita than those infected with IJs as compared with positive control. While, oxamyl treatment gave the best results in pots infected by eggs and IJs.The lowest galling (gall index), number of eggs and juveniles in soil was observed in the treatment with mixture of Serratia spp. and Pseudomonas spp. as well as, enhanced growth of sponge gourd more than application each of them alone. Pots treated with oxamyl overwhelmed those treated with mixture of Serratia spp. and Pseudomonas spp.     

DYn-2 Based Identification of Arabidopsis Sulfenomes

Identifying the sulfenylation state of stressed cells is emerging as a strategic approach for the detection of key reactive oxygen species signaling proteins. Here, we optimized an in vivo trapping method for cysteine sulfenic acids in hydrogen peroxide (H₂O₂) stressed plant cells using a dimedone based DYn-2 probe. We demonstrated that DYn-2 specifically detects sulfenylation events in an H₂O₂ dose- and time-dependent way. With mass spectrometry, we identified 226 sulfenylated proteins after H₂O₂ treatment of Arabidopsis cells, residing in the cytoplasm (123); plastid (68); mitochondria (14); nucleus (10); endoplasmic reticulum, Golgi and plasma membrane (7) and peroxisomes (4). Of these, 123 sulfenylated proteins have never been reported before to undergo cysteine oxidative post-translational modifications in plants. All in all, with this DYn-2 approach, we have identified new sulfenylated proteins, and gave a first glance on the locations of the sulfenomes of Arabidopsis thaliana.Among the different amino acids, the sulfur containing amino acids like cysteine are particularly susceptible to oxidation by reactive oxygen species (ROS)¹ (1, 2). Recent studies suggest that the sulfenome, the initial oxidation products of cysteine residues, functions as an intermediate state of redox signaling (3 –5). Thus, identifying the sulfenome under oxidative stress is a way to detect potential redox sensors (6, 7).This central role of the sulfenome in redox signaling provoked chemical biologists to develop strategies for sensitive detection and identification of sulfenylated proteins. The in situ trapping of the sulfenome is challenging because of two major factors: (1) the highly reactive, transient nature of sulfenic acids, which might be over-oxidized in excess of ROS, unless immediately protected by disulfide formation (7); (2) the intracellular compartmentalization of the redox state that might be disrupted during extraction procedures, resulting in artificial non-native protein oxidations (8, 9). Having a sulfur oxidation state of zero, sulfenic acids can react as both electrophile and nucleophile, however, direct detection methods are based on the electrophilic character of sulfenic acid (10). In 1974, Allison and coworkers reported a condensation reaction between the electrophilic sulfenic acid and the nucleophile dimedone (5,5-dimethyl-1,3-cyclohexanedione), producing a corresponding thioether derivative (11). This chemistry is highly selective and, since then, has been exploited to detect dimedone modified sulfenic acids using mass spectrometry (12). However, dimedone has limited applications for cellular sulfenome identification because of the lack of a functional group to enrich the dimedone tagged sulfenic acids. Later, dimedone-biotin/fluorophores conjugates have been developed, which allowed sensitive detection and enrichment of sulfenic acid modified proteins (13 –15). This approach, however, was not always compatible with in vivo cellular sulfenome analysis, because the biotin/fluorophores-conjugated dimedone is membrane impermeable (9) and endogenous biotinylated proteins might appear as false positives.More recently, the Carroll lab has developed DYn-2, a sulfenic acid specific chemical probe. This chemical probe consists of two functional units: a dimedone scaffold for sulfenic acid recognition and an alkyne chemical handle for enrichment of labeled proteins (9). Once the sulfenic acids are tagged with the DYn-2 probe, they can be biotinylated through click chemistry (16). The click reaction used here is a copper (I)-catalyzed azide-alkyne cycloaddition reaction (17), also known as azide-alkyne Huisgen cycloaddition (16). With this chemistry, a complex is formed between the alkyne functionalized DYn-2 and the azide functionalized biotin. This biotin functional group facilitates downstream detection, enrichment, and mass spectrometry based identification (Fig. 1). In an evaluation experiment, DYn-2 was found to efficiently detect H₂O₂-dependent sulfenic acid modifications in recombinant glutathione peroxidase 3 (Gpx3) of budding yeast (18). Moreover, it was reported that DYn-2 is membrane permeable, non-toxic, and a non-influencer of the intracellular redox balance (17, 18). Therefore, DYn-2 has been suggested as a global sulfenome reader in living cells (17, 18), and has been applied to investigate epidermal growth factor (EGF) mediated protein sulfenylation in a human epidermoid carcinoma A431 cell line and to identify intracellular protein targets of H₂O₂ during cell signaling (17).Open in a separate windowFig. 1.Schematic views of the molecular mechanism of the DYn-2 probe and the strategy to identify DYn-2 trapped sulfenylated proteins. A, DYn-2 specifically detects sulfenic acid modifications, but no other thiol modifications. B, Biotinylation of the DYn-2 tagged proteins by click reaction. C, Once DYn-2 tagged proteins are biotinylated, a streptavidin-HRP (Strep-HRP) blot visualizes sulfenylation, or alternatively, after enrichment on avidin beads, proteins are identified by mass spectrometry analysis.Here, we selected the DYn-2 probe to identify the sulfenome in plant cells under oxidative stress. Through a combination of biochemical, immunoblot and mass spectrometry techniques, and TAIR10 database and SUBA3-software predictions, we can claim that DYn-2 is able to detect sulfenic acids on proteins located in different subcellular compartments of plant cells. We identified 226 sulfenylated proteins in response to an H₂O₂ treatment of Arabidopsis cell suspensions, of which 123 proteins are new candidates for cysteine oxidative post-translational modification (PTM) events.     

Nematicidal activity of Haplophyllum tuberculatum and Plectranthus cylindraceus oils against Meloidogyne javanica

The potentials of Haplophyllum tuberculatum and Plectranthus cylindraceus oils to control Meloidogyne javanica were investigated in vitro and in a greenhouse. A mixture of Haplophyllum and Plectranthus oils (1:1) was highly toxic to M. javanica in vitro, as it killed all nematode juveniles and inhibited hatching of eggs at 12.5 μg/ml concentration after 24 h exposure time, as did carbofuran at the same concentration. In the green-house, tomatoes grown in soil treated with a combination (1:1) of the two oils developed fewer root galls than those grown in soil treated with higher doses of either oil. The oil mixture, at 2.5 and 5.0 μg/ml of soil, was not phytotoxic to tomato plants as evident from the appearance and height of plants after 12 weeks exposure time, compared to treatment over the same period at lower effective doses. The nematicidal activity of the combined essential oils was suggested by the presence of C₁₀ dienes, C₁₀ trienes and C₁₀ phenol.     

Effect of Low-Level Laser on Some Metals Related to Redox State and Histological Alterations in the Liver and Kidney of Irradiated Rats

Biological Trace Element Research - This report explains the employing of a combination test of traditional cell culture with a quantitative real-time PCR for assessment of the antiviral effect of...     

Soil anammox community structure in different land use soils treatment with 13 C urea as determined by analysis of phospholipid fatty acids

The anaerobic ammonium oxidation (anammox) process is globally an important nitrogen-cycling process mediated by specialized microbes. However, still little information is documented about anammox microbial community structure under agricultural soils. The anaerobic incubation experiment was conducted to study the impacts of different land use soils fertilized by 13C-urea on the activity and diversity of anammox bacteria using stable isotope to probe the phospholipid fatty acid (PLFA-SIP). The 13C was preferentially incorporated in ratios PLFAs 16:1ω7c, 16:1ω5c, and 16:0. The results revealed that the abundance of the anammox bacteria (both hzs-β and hzo) were observed in vegetable soil V1 and paddy soils (R1 and R2) means that they were positively correlated with 13C-urea but were negatively correlated with NO3 −-N and NH4 +-N concentrations. Thus, 13C-PLFAs 16:1ω7c, 16:1ω5c, and 16:0 could be the biomarker as soil anammox. The anaerobic microbial community composition of soils under different land use systems was diverse, and V1, R1, and R2 had similar microbial diversity and higher microbial biomass. The principal component analysis between soil properties and gene abundance suggested that not only pH but also soil organic matter, available P, and available K were important factors for the anammox process. This study suggested that 13C-Urea-PLFA for anaerobic incubation was a simple method to study anammox microbial community structure through affecting the soil nutrients, and the different land use systems played important roles in determining the microbial composition of soils.