Metabolomics and dereplication strategies in the discovery of natural product derived drugs

Metabolomics is the technology designed to provide general qualitative and quantitative profile of metabolites in organisms exposed to different conditions. Metabolomics is applied in many aspects of natural drug discoveries, particularly in bioactivity screening to improve dereplication and identification procedures. Fast dereplication of known compounds and identification of lead bioactive metabolites is important in the primary stages of metabolomics profiling prior to an intensive isolation work. Two levels of metabolomics were used in this study. First was metabolites fingerprinting which aimed for rapid classification of samples by comparing the metabolites patterns or fingerprints. Second was metabolites profiling and dereplication study for class of compounds related to a specific pathway in order to individually identify and quantify these metabolites. This study involved isolation of endophytic fungus Aspergillus aculeatus from Egyptian medicinal plants, Terminalia laxiflora. Identification of the strains has been achieved through molecular biological methods. Metabolomic profiling, using NMR and HR-MS were done at different stages of the growth phase for both solid and liquid culture media. Dereplication studies were accomplished by utilizing the MZmine 2.10 software with aid of the AntiBase and DNP databases. By end of the dereplication process metabolites were sorted out into three levels; level 1: identified compounds, level 2: putatively annotated compound class and level 3: completely unidentified and unclassified compounds. Multivariate data analysis was employed by using PCA in order to classify samples into groups, trends and outliers, which maximize the information, can be obtained from spectral data. OPLS-DA was used to correlate the chemical profile with tested biological activity. Metabolomics has been shown to be a powerful facilitator in the discovery of natural products, which are considered an excellent source for novel leads

Effects of quantum gravity on the inflationary parameters and thermodynamics of the early universe

The effects of generalized uncertainty principle (GUP) on the inflationary dynamics and the thermodynamics of the early universe are studied. Using the GUP approach, the tensorial and scalar density fluctuations in the inflation era are evaluated and compared with the standard case. We find a good agreement with the Wilkinson Microwave Anisotropy Probe data. Assuming that a quantum gas of scalar particles is confined within a thin layer near the apparent horizon of the Friedmann-Lemaitre-Robertson-Walker universe which satisfies the boundary condition, the number and entropy densities and the free energy arising form the quantum states are calculated using the GUP approach. A qualitative estimation for effects of the quantum gravity on all these thermodynamic quantities is introduced.Comment: 15 graghes, 7 figures with 17 eps graph

Use of humanised rat basophilic leukaemia cell line RS-ATL8 for the assessment of allergenicity of Schistosoma mansoni proteins.

BACKGROUND Parasite-specific IgE is thought to correlate with protection against Schistosoma mansoni infection or re-infection. Only a few molecular targets of the IgE response in S. mansoni infection have been characterised. A better insight into the basic mechanisms of anti-parasite immunity could be gained from a genome-wide characterisation of such S. mansoni allergens. This would have repercussions on our understanding of allergy and the development of safe and efficacious vaccinations against helminthic parasites. METHODOLOGY/PRINCIPAL FINDINGS A complete medium- to high-throughput amenable workflow, including important quality controls, is described, which enables the rapid translation of S. mansoni proteins using wheat germ lysate and subsequent assessment of potential allergenicity with a humanised Rat Basophilic Leukemia (RBL) reporter cell line. Cell-free translation is completed within 90 minutes, generating sufficient amounts of parasitic protein for rapid screening of allergenicity without any need for purification. Antigenic integrity is demonstrated using Western Blotting. After overnight incubation with infected individuals' serum, the RS-ATL8 reporter cell line is challenged with the complete wheat germ translation mixture and Luciferase activity measured, reporting cellular activation by the suspected allergen. The suitability of this system for characterization of novel S. mansoni allergens is demonstrated using well characterised plant and parasitic allergens such as Par j 2, SmTAL-1 and the IgE binding factor IPSE/alpha-1, expressed in wheat germ lysates and/or E. coli. SmTAL-1, but not SmTAL2 (used as a negative control), was able to activate the basophil reporter cell line. CONCLUSION/SIGNIFICANCE This method offers an accessible way for assessment of potential allergenicity of anti-helminthic vaccine candidates and is suitable for medium- to high-throughput studies using infected individual sera. It is also suitable for the study of the basis of allergenicity of helminthic proteins

Laparoscopy in management of appendicitis in high-, middle-, and low-income countries: a multicenter, prospective, cohort study.

BACKGROUND: Appendicitis is the most common abdominal surgical emergency worldwide. Differences between high- and low-income settings in the availability of laparoscopic appendectomy, alternative management choices, and outcomes are poorly described. The aim was to identify variation in surgical management and outcomes of appendicitis within low-, middle-, and high-Human Development Index (HDI) countries worldwide. METHODS: This is a multicenter, international prospective cohort study. Consecutive sampling of patients undergoing emergency appendectomy over 6 months was conducted. Follow-up lasted 30 days. RESULTS: 4546 patients from 52 countries underwent appendectomy (2499 high-, 1540 middle-, and 507 low-HDI groups). Surgical site infection (SSI) rates were higher in low-HDI (OR 2.57, 95% CI 1.33-4.99, p = 0.005) but not middle-HDI countries (OR 1.38, 95% CI 0.76-2.52, p = 0.291), compared with high-HDI countries after adjustment. A laparoscopic approach was common in high-HDI countries (1693/2499, 67.7%), but infrequent in low-HDI (41/507, 8.1%) and middle-HDI (132/1540, 8.6%) groups. After accounting for case-mix, laparoscopy was still associated with fewer overall complications (OR 0.55, 95% CI 0.42-0.71, p < 0.001) and SSIs (OR 0.22, 95% CI 0.14-0.33, p < 0.001). In propensity-score matched groups within low-/middle-HDI countries, laparoscopy was still associated with fewer overall complications (OR 0.23 95% CI 0.11-0.44) and SSI (OR 0.21 95% CI 0.09-0.45). CONCLUSION: A laparoscopic approach is associated with better outcomes and availability appears to differ by country HDI. Despite the profound clinical, operational, and financial barriers to its widespread introduction, laparoscopy could significantly improve outcomes for patients in low-resource environments. TRIAL REGISTRATION: NCT02179112

Pooled analysis of WHO Surgical Safety Checklist use and mortality after emergency laparotomy

Background The World Health Organization (WHO) Surgical Safety Checklist has fostered safe practice for 10 years, yet its place in emergency surgery has not been assessed on a global scale. The aim of this study was to evaluate reported checklist use in emergency settings and examine the relationship with perioperative mortality in patients who had emergency laparotomy. Methods In two multinational cohort studies, adults undergoing emergency laparotomy were compared with those having elective gastrointestinal surgery. Relationships between reported checklist use and mortality were determined using multivariable logistic regression and bootstrapped simulation. Results Of 12 296 patients included from 76 countries, 4843 underwent emergency laparotomy. After adjusting for patient and disease factors, checklist use before emergency laparotomy was more common in countries with a high Human Development Index (HDI) (2455 of 2741, 89.6 per cent) compared with that in countries with a middle (753 of 1242, 60.6 per cent; odds ratio (OR) 0.17, 95 per cent c.i. 0.14 to 0.21, P <0001) or low (363 of 860, 422 per cent; OR 008, 007 to 010, P <0.001) HDI. Checklist use was less common in elective surgery than for emergency laparotomy in high-HDI countries (risk difference -94 (95 per cent c.i. -11.9 to -6.9) per cent; P <0001), but the relationship was reversed in low-HDI countries (+121 (+7.0 to +173) per cent; P <0001). In multivariable models, checklist use was associated with a lower 30-day perioperative mortality (OR 0.60, 0.50 to 073; P <0.001). The greatest absolute benefit was seen for emergency surgery in low- and middle-HDI countries. Conclusion Checklist use in emergency laparotomy was associated with a significantly lower perioperative mortality rate. Checklist use in low-HDI countries was half that in high-HDI countries.Peer reviewe

Beam Energy Dependence of Jet-Quenching Effects in Au plus Au Collisions at root s(NN)=7.7, 11.5, 14.5, 19.6, 27, 39, and 62.4 GeV

We report measurements of the nuclear modification factor, $R_{ \mathrm{CP}}$, for charged hadrons as well as identified $\pi^{+(-)}$, $K^{+(-)}$, and $p(\overline{p})$ for Au+Au collision energies of $\sqrt{s_{_{ \mathrm{NN}}}}$ = 7.7, 11.5, 14.5, 19.6, 27, 39, and 62.4 GeV. We observe a clear high-$p_{\mathrm{T}}$ net suppression in central collisions at 62.4 GeV for charged hadrons which evolves smoothly to a large net enhancement at lower energies. This trend is driven by the evolution of the pion spectra, but is also very similar for the kaon spectra. While the magnitude of the proton $R_{ \mathrm{CP}}$ at high $p_{\mathrm{T}}$ does depend on collision energy, neither the proton nor the anti-proton $R_{ \mathrm{CP}}$ at high $p_{\mathrm{T}}$ exhibit net suppression at any energy. A study of how the binary collision scaled high-$p_{\mathrm{T}}$ yield evolves with centrality reveals a non-monotonic shape that is consistent with the idea that jet-quenching is increasing faster than the combined phenomena that lead to enhancement.We report measurements of the nuclear modification factor RCP for charged hadrons as well as identified π+(-), K+(-), and p(p¯) for Au+Au collision energies of sNN=7.7, 11.5, 14.5, 19.6, 27, 39, and 62.4 GeV. We observe a clear high-pT net suppression in central collisions at 62.4 GeV for charged hadrons which evolves smoothly to a large net enhancement at lower energies. This trend is driven by the evolution of the pion spectra but is also very similar for the kaon spectra. While the magnitude of the proton RCP at high pT does depend on the collision energy, neither the proton nor the antiproton RCP at high pT exhibit net suppression at any energy. A study of how the binary collision-scaled high-pT yield evolves with centrality reveals a nonmonotonic shape that is consistent with the idea that jet quenching is increasing faster than the combined phenomena that lead to enhancement