Rapid detection of resistance in Staphylococcus aureus by using Quicolor ES

Traditional microbiological methods are dependent on the growth of microorganisms, and hence require prolonged periods. The methods used to detect resistance in Staphylococcus aureus should have high sensitivity and specificity, yet provide results in a timely manner. The aim of this study was to evaluate the use of Quicolor (QC) ES^® agar for the rapid detection of resistance in S. aureus. We evaluated 100 clinical S. aureus isolates. Resistance detection was performed using traditional microbiological methods. Methicillin resistance detection was evaluated using traditional and molecular microbiological methods. Traditional antibiotic susceptibility testing methods, such as disc diffusion, were conducted using QC ES and Mueller–Hinton (MH) media. The plates were incubated at 36 °C for 5, 6 and 24 h. Rapid results obtained using QC ES agar after 5 h of incubation were consistent with those using the overnight procedure with MH agar for 83 of the 100 S. aureus (including methicillin-susceptible S. aureus) strains. However, the correlation for oxacillin between MH (24 h) and QC ES (5 h) was not satisfactory (r = 0.770). The total agreement between QC ES and MH agar was 83 % after 5 h, 89 % after 6 h, and 94 % after 24 h. The accurate and rapid detection of resistance in S. aureus is critical due to the associated therapeutic problems and infection control measures. We believe that the use of QC ES for S. aureus will reduce the delay in resistance detection, thus providing physicians and infection control practitioners with early information for better management.     

Influence of hydrophobic and electrostatic residues on SARS‐coronavirus S2 protein stability: Insights into mechanisms of general viral fusion and inhibitor design

Severe acute respiratory syndrome (SARS) is an acute respiratory disease caused by the SARS‐coronavirus (SARS‐CoV). SARS‐CoV entry is facilitated by the spike protein (S), which consists of an N‐terminal domain (S1) responsible for cellular attachment and a C‐terminal domain (S2) that mediates viral and host cell membrane fusion. The SARS‐CoV S2 is a potential drug target, as peptidomimetics against S2 act as potent fusion inhibitors. In this study, site‐directed mutagenesis and thermal stability experiments on electrostatic, hydrophobic, and polar residues to dissect their roles in stabilizing the S2 postfusion conformation was performed. It was shown that unlike the pH‐independent retroviral fusion proteins, SARS‐CoV S2 is stable over a wide pH range, supporting its ability to fuse at both the plasma membrane and endosome. A comprehensive SARS‐CoV S2 analysis showed that specific hydrophobic positions at the C‐terminal end of the HR2, rather than electrostatics are critical for fusion protein stabilization. Disruption of the conserved C‐terminal hydrophobic residues destabilized the fusion core and reduced the melting temperature by 30°C. The importance of the C‐terminal hydrophobic residues led us to identify a 42‐residue substructure on the central core that is structurally conserved in all existing CoV S2 fusion proteins (root mean squared deviation = 0.4 Å). This is the first study to identify such a conserved substructure and likely represents a common foundation to facilitate viral fusion. We have discussed the role of key residues in the design of fusion inhibitors and the potential of the substructure as a general target for the development of novel therapeutics against CoV infections.     

Neonatal Injury at Cephalic Vaginal Delivery: A Retrospective Analysis of Extent of Association with Shoulder Dystocia

Purpose

To describe the risk factors and labor characteristics of Clavicular fracture (CF) and brachial plexus injury (BPI); and compare antenatal and labor characteristics and prognosis of obstetrical BPI associated with shoulder dystocia with obstetrical BPI not associated with shoulder dystocia.

Methods

This retrospective study consisted of women who gave birth to an infant with a fractured clavicle or BPI between January 2009 and June 2013. Antenatal and neonatal data were compared between groups. The control group (1300) was composed of the four singleton vaginal deliveries that immediately followed each birth injury. A multivariable logistic regression model, with backward elimination, was constructed in order to find independent risk factors associated with BPI and CF. A subgroup analysis involved comparison of features of BPI cases with or without associated shoulder dystocia.

Results

During the study period, the total number of vaginal deliveries was 44092. The rates of CF, BPI and shoulder dystocia during the study period were 0,6%, 0,16% and 0,29%, respectively. In the logistic regression model, shoulder dystocia, GDM, multiparity, gestational age >42 weeks, protracted labor, short second stage of labor and fetal birth weight greater than 4250 grams increased the risk of CF independently. Shoulder dystocia and protracted labor were independently associated with BPI when controlled for other factors. Among neonates with BPI whose injury was not associated with shoulder dystocia, five (12.2%) sustained permanent injury, whereas one neonate (4.5%) with BPI following shoulder dystocia sustained permanent injury (p = 0.34).

Conclusion

BPI not associated with shoulder dystocia might have a higher rate of concomitant CF and permanent sequelae.     

Flux balancing of light and nutrients in a biofilm photobioreactor for maximizing photosynthetic productivity

This article reports a combined experimental and numerical study on the efficient operation of Porous Substrate Bioreactors. A comprehensive model integrating light transport, mass transport, and algal growth kinetics was used to understand the productivity of photosynthetic biofilms in response to delivery rates of photons and nutrients. The reactor under consideration was an evaporation driven Porous Substrate Bioreactor (PSBR) cultivating the cyanobacteria Anabaena variabilis as a biofilm on a porous substrate which delivers water and nutrients to the cells. In an unoptimized experimental case, this reactor was operated with a photosynthetic efficiency of 2.3%, competitive with conventional photobioreactors. Moreover, through a scaling analysis, the location at which the phosphate delivery rate decreased the growth rate to half of its uninhibited value was predicted as a function of microorganism and bioreactor properties. The numerical model along with the flux balancing techniques presented herein can serve as tools for designing and selecting operating parameters of biofilm based cultivation systems for maximum productivity. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:348–359, 2014     

Therapeutic Potential of Some Plant Extracts Used in Turkish Traditional Medicine on Streptozocin-Induced Type 1 Diabetes Mellitus in Rats

Diabetes mellitus (DM) is known to impair many physiological functions. Some reports claim that medicinal plants can reduce these alterations caused by DM. The aim of this study was to investigate the therapeutic potential of aqueous-methanol extracts of Urtica dioica, Thymus vulgaris (TV), Myrtus communis (MC), Scolymus hispanicus (SH) and Cinnamomun zeylanicum (CZ) on streptozotocin (STZ)-induced type 1 DM in rats. Diabetes was induced via a single i.p. injection of STZ (65 mg/kg body weight). After 1 week to allow for development of diabetes, each plant extract was administered to diabetic rats separately at a dose of 100 mg/kg body weight daily for 28 days. The results showed that only SH extract significantly (P < 0.05) amended fasting blood glucose level. The lipid profile was ameliorated especially by supplementations of TV, MC and CZ extracts. Almost all plant extract treatments markedly (P < 0.05) increased reduced glutathione content and decreased lipid peroxidation levels of erythrocyte, plasma, retina and lens tissues. They also significantly (P < 0.05) amended erythrocyte catalase activity, levels of marker serum enzymes (except amylase), urea and blood urea nitrogen when compared to diabetic rats treated with nothing. Furthermore, none of the plant extracts counteracted body weight loss of diabetic rats. Our data revealed that the aforementioned plant extracts have remarkable potential to counteract DM-caused alterations, probably through their antioxidant and free radical-defusing effects.     

Identification of common root-lesion nematode (Pratylenchus thornei Sher et Allen) loci in bread wheat.

Plant parasitic nematodes are a major biotic cause of wheat-yield loss in temperate wheat-growing regions. A major strategy to develop resistance to root-lesion nematodes (RLNs) in wheat is to assess and then exploit their natural genetic variation. This study examines RLN (Pratylenchus thornei) resistance in 1 Middle Eastern landrace (AUS4930 7.2) and 1 synthetic hexaploid wheat, CROC_1/AE.SQUARROSA (224)//OPATA (CROC), using F2 and F9 populations generated by crossing AUS4930 7.2 and CROC with the susceptible cultivar Pastor, and inoculating these crosses with P. thornei in greenhouse trials. Wheat microsatellite markers linked to previously identified quantitative trait loci (QTLs) for resistance to P. thornei and P. neglectus were used to screen both populations. In the AUS4930 7.2 x Pastor population, resistance loci on chromosomes 1B, 2B, and 6D were detected. Similarly, in the CROC x Pastor population, 2 resistance loci, located on chromosomes 1B and 3B, were identified. Interestingly, a resistance locus located on chromosome 6D was not detected. More detailed mapping is required in these 2 populations, developed using new RLN resistance sources, to determine whether the QTLs identified on these chromosomes are the same, are allelic, or are linked to different resistance loci from those previously identified, and to determine whether these 2 sources contain other novel resistance loci.     

99mTc-HMPAO labelling inhibits cell motility and cell proliferation and induces apoptosis of NC-NC cells

(99m)Tc-hexamethyl-propylenamine-oxime ((99m)Tc-HMPAO)-labelled leukocytes have been used in standard diagnostic procedures for the detection of infection and inflammation. Although some investigators have already pointed out that labelling of leukocytes with (99m)Tc-HMPAO has detrimental effects on the cells, still very little is known regarding the effects of ionizing radiation on lymphocyte function. The effects of (99m)Tc-HMPAO-labelling on lymphocyte adhesion, proliferation, mitotic index, migration and apoptosis were evaluated. The lymphoblastoid cell line NC-NC was used as the lymphocyte population. (99m)Tc-HMPAO-labelling decreased cell adhesion, proliferation, mitotic index and motility, whereas it induced apoptosis and cell-cycle arrest. The rate of decrease in cell proliferation was up to 70% (P<0.001) by day 4 after labelling. (99m)Tc-HMPAO-labelling led a 35% decrease (P<0.001) in adhesion ability of the cells on fibronectin at 16h. Using the Boyden chamber motility assay, it was shown that both spontaneous and monocyte chemotactic protein (MCP-1)-induced lymphocyte motility were strongly reduced by (99m)Tc-HMPAO-labelling. The decrease in motility was approximately five-fold (P<0.05). In addition, a 12-fold increase (P<0.05) was observed in apoptosis of the (99m)Tc-HMPAO-treated cells compared with control cells. Besides, it was shown that cell-cycle arrest was induced starting from the 3rd day after treatment with (99m)Tc-HMPAO. Our observations indicate that (99m)Tc-HMPAO-labelling has damaging effects on lymphocyte function including cell adhesion, proliferation, mitotic index, motility and cell cycle under in vitro conditions.     

New SIRT2 inhibitors: Histidine-based bleomycin spin-off

Bleomycin is considered to exert its antitumor activity via DNA cleavage mediated by activated oxygen generated from the iron complex in its chelator moiety. Spin-offs from this moiety, HPH-1Trt and HPH-2Trt, with anti-cancer activities were recently synthesized. In this paper, we developed inhibitors of nicotinamide adenine dinucleotide-dependent deacetylase isoform 2 of Sirtuin protein (SIRT2), based on HPH-1Trt/HPH-2Trt, and aimed to generate new anti-cancer drugs. HPH-1Trt and HPH-2Trt had in vitro anti-SIRT2 inhibitory activity with 50% inhibitory concentration (IC₅₀) values of 5.5 and 8.8?μM, respectively. A structural portion of HPH-1Trt/HPH-2Trt, a tritylhistidine derivative TH-1, had stronger activity (IC₅₀?=?1.7?μM), and thus, fourteen derivatives of TH-1 were synthesized. Among them, TH-3 had the strongest activity (IC₅₀?=?1.3?μM). Selective binding of TH-3 in the pocket of SIRT2 protein was confirmed with a molecular docking study. Furthermore, TH-3 strongly lowered viability of the breast cancer cell line MCF7 with an IC₅₀ of 0.71?μM. A structure-activity relationship study using cell lines suggested that the mechanism of TH-3 to suppress MCF7 cells involves not only SIRT2 inhibition, but also another function. This compound may be a new candidate anti-cancer drug.     

PRER: A patient representation with pairwise relative expression of proteins on biological networks

Changes in protein and gene expression levels are often used as features in predictive modeling such as survival prediction. A common strategy to aggregate information contained in individual proteins is to integrate the expression levels with the biological networks. In this work, we propose a novel patient representation where we integrate proteins’ expression levels with the protein-protein interaction (PPI) networks: Patient representation with PRER (Pairwise Relative Expressions with Random walks). PRER captures the dysregulation patterns of proteins based on the neighborhood of a protein in the PPI network. Specifically, PRER computes a feature vector for a patient by comparing the source protein’s expression level with other proteins’ levels that are within its neighborhood. The neighborhood of the source protein is derived by biased random-walk strategy on the network. We test PRER’s performance in survival prediction task in 10 different cancers using random forest survival models. PRER yields a statistically significant predictive performance in 9 out of 10 cancers when compared to the same model trained with features based on individual protein expressions. Furthermore, we identified the pairs of proteins that their interactions are predictive of patient survival but their individual expression levels are not. The set of identified relations provides a valuable collection of protein biomarkers with high prognostic value. PRER can be used for other complex diseases and prediction tasks that use molecular expression profiles as input. PRER is freely available at: https://github.com/hikuru/PRER.