Similarity search combined with docking and molecular dynamics for novel hAChE inhibitor scaffolds

The main purpose of this study was to address the performance of virtual screening methods based on ligands and the protein structure of acetylcholinesterase (AChE) in order to retrieve novel human AChE (hAChE) inhibitors. In addition, a protocol was developed to identify novel hit compounds and propose new promising AChE inhibitors from the ZINC database with 10 million commercially available compounds. In this sense, 3D similarity searches using rapid overlay of chemical structures and similarity analysis through comparison of electrostatic overlay of docked hits were used to retrieve AChE inhibitors from collected databases. Molecular dynamics simulation of 100 ns was carried out to study the best docked compounds from similarity searches. Some key residues were identified as crucial for the dual binding mode of inhibitor with the interaction site. All results indicated the relevant use of EON and docking strategy for identifying novel hit compounds as promising potential anticholinesterase candidates, and seven new structures were selected as potential hAChE inhibitors.

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Graphical abstract Compound N01 in the 4M0E hAChE crystallography structure from docking results. Yellow dashed lines Hydrogen bonds, blue dashed lines π-stacking interactions, green dashed lines cation-π interactions.

     

Excitonic connectivity between photosystem II units: what is it, and how to measure it?

In photosynthetic organisms, light energy is absorbed by a complex network of chromophores embedded in light-harvesting antenna complexes. In photosystem II (PSII), the excitation energy from the antenna is transferred very efficiently to an active reaction center (RC) (i.e., with oxidized primary quinone acceptor Q _A), where the photochemistry begins, leading to O₂ evolution, and reduction of plastoquinones. A very small part of the excitation energy is dissipated as fluorescence and heat. Measurements on chlorophyll (Chl) fluorescence and oxygen have shown that a nonlinear (hyperbolic) relationship exists between the fluorescence yield (Φ _F ) (or the oxygen emission yield, $ \Phi _{{{\text{O}}_{2} }} $ ) and the fraction of closed PSII RCs (i.e., with reduced Q _A). This nonlinearity is assumed to be related to the transfer of the excitation energy from a closed PSII RC to an open (active) PSII RC, a process called PSII excitonic connectivity by Joliot and Joliot (CR Acad Sci Paris 258: 4622–4625, 1964). Different theoretical approaches of the PSII excitonic connectivity, and experimental methods used to measure it, are discussed in this review. In addition, we present alternative explanations of the observed sigmoidicity of the fluorescence induction and oxygen evolution curves.     

Influence of Flexibility and Variability of Working Hours on Health and Well‐Being

Flexible working hours can have several meanings and can be arranged in a number of ways to suit the worker and/or employer. Two aspects of “flexible” arrangement of working hours were considered: one more subjected to company control and decision (variability) and one more connected to individual discretion and autonomy (flexibility). The aim of the study was to analyze these two dimensions in relation to health and well‐being, taking into consideration the interaction with some relevant background variables related to demographics plus working and social conditions. The dataset of the Third European Survey on working conditions, conducted in 2000 and involving 21,505 workers, was used. Nineteen health disorders and four psycho‐social conditions were tested by means of multiple logistic regression analysis, in which mutually adjusted odds ratios were calculated for age, gender, marital status, number of children, occupation, mode of employment, shift work, night work, time pressure, mental and physical workload, job satisfaction, and participation in work organization. The flexibility and variability of working hours appeared inversely related to health and psycho‐social well‐being: the most favorable effects were associated with higher flexibility and lower variability. The analysis of the interactions with the twelve intervening variables showed that physical work, age, and flexibility are the three most important factors affecting health and well‐being. Flexibility resulted as the most important factor to influence work satisfaction; the second to affect family and social commitment and the ability to do the same job when 60 years old, as well as trauma, overall fatigue, irritability, and headache; and the third to influence heart disease, stomachache, anxiety, injury, and the feeling that health being at risk because of work. Variability was the third most important factor influencing family and social commitments. Moreover, shift and night work confirmed to have a significant influence on sleep, digestive and cardiovascular troubles, as well and health and safety at work. Time pressure also showed a relevant influence, both on individual stress and social life. Therefore, suitable arrangements of flexible working time, aimed at supporting workers' coping strategies, appear to have a clear beneficial effect on worker health and well‐being, with positive consequences also at the company and social level, as evidenced by the higher “feeling to be able to work until 60 years of age”.     

Coagulation Activation in Children with Sickle Cell Disease Is Associated with Cerebral Small Vessel Vasculopathy

Background

Thrombotic complications in Sickle Cell Disease (SCD) arise since infancy, but the role of the coagulation system in children has been poorly explored. To determine its role in the development of clinical complications in childhood we measured coagulation and endothelial parameters in children with SCD at steady state.

Methods

Markers of thrombin generation, fibrin dissolution and endothelial activation were evaluated in 38 children with SS-Sβ°, 6 with SC disease and 50 age and blood group matched controls. Coagulation variables were correlated with markers of hemolysis and inflammation, with the presence of cerebral and lung vasculopathy and with the frequency of clinical complications.

Results

SS-Sβ° patients presented higher levels of factor VIII, von Willebrand factor antigen (VWF:Ag) and collagen binding activity, tissue plasminogen activator antigen (t-PA:Ag), D-dimer, p-selectin, prothrombin fragment1+2 (F1+2) and lower ADAMTS-13:activity/VWF:Ag (p<0.05) compared to controls and SC patients. In SS-Sβ° patients coagulation variables correlated positively with markers of inflammation, hemolysis, and negatively with HbF (p<0.05). Patients with cerebral silent infarcts showed significant decrease in t-PA:Ag and ADAMTS-13 Antigen and a tendency toward higher D-dimer, F1+2, TAT compared to patients without them. D-dimer was associated with a six fold increased risk of cerebral silent infarcts. No correlation was found between coagulation activation and large vessel vasculopathy or other clinical events except for decreased t-PA:Ag in patients with tricuspid Rigurgitant Velocity >2.5m/sec.

Conclusions

SS-Sβ° disease is associated with extensive activation of the coagulation system at steady state since young age. ADAMTS-13 and t-PA:Ag are involved in the development of cerebral silent infarcts.     

Detection of MicroRNAs in Archival Cytology Urine Smears

MicroRNAs’ dysregulation and profiling have been demonstrated to be clinically relevant in urothelial carcinoma (UC). Urine cytology is commonly used as the mainstay non-invasive test for secondary prevention and follow-up of UC patients. Ancillary tools are needed to support cytopathologists in the diagnosis of low-grade UC. The feasibility and reliability of microRNAs profiling by qRT-PCR analysis (miR-145 and miR-205) in archival routine urine cytology smears (affected by fixation/staining [Papanicolau] and room temperature storage) was tested in a series of 15 non-neoplastic and 10 UC urine specimens. Only samples with >5,000 urothelial cells and with <50% of inflammatory cells/red blood cells clusters were considered. Overall, a satisfactory amount of total RNA was obtained from all the considered samples (mean 1.27±1.43 µg, range 0.06–4.60 µg). Twenty nanograms of total RNA have been calculated to be the minimal total RNA concentration for reliable and reproducible miRNAs expression profiling analysis of archival cytological smears (slope = -3.4084; R-squared = 0.99; efficiency = 1.94). miR-145 and miR-205 were significantly downregulated in UC samples in comparison to non-tumor controls. These findings demonstrate that urine archival cytology smears are suitable for obtaining high-quality RNA to be used in microRNAs expression profiling. Further studies should investigate if miRNAs profiling can be successfully translated into clinical practice as diagnostic or prognostic markers.     

Resistance to experimental autoimmune encephalomyelitis development in Lewis rats from a conventional animal facility

Experimental autoimmune encephalomyelitis (EAE) is an inflammatory disease of the brain and spinal cord that is mediated by CD4+ T lymphocytes specific to myelin components. In this study we compared development of EAE in Lewis rats from two colonies, one kept in pathogen-free conditions (CEMIB colony) and the other (Botucatu colony) kept in a conventional animal facility. Female Lewis rats were immunized with 100 microl of an emulsion containing 50 microg of myelin, associated with incomplete Freund's adjuvant plus Mycobacterium butyricum. Animals were daily evaluated for clinical score and weight. CEMIB colony presented high EAE incidence with clinical scores that varied from three to four along with significant weight losses. A variable disease incidence was observed in the Botucatu colony with clinical scores not higher than one and no weight loss. Immunological and histopathological characteristics were also compared after 20 days of immunization. Significant amounts of IFN-gamma, TNF-alpha and IL-10 were induced by myelin in cultures from CEMIB animals but not from the Botucatu colony. Significantly higher levels of anti-myelin IgG1 were detected in the CEMIB colony. Clear histopathological differences were also found. Cervical spinal cord sections from CEMIB animals showed typical perivascular inflammatory foci whereas samples from the Botucatu colony showed a scanty inflammatory infiltration. Helminths were found in animals from Botucatu colony but not, as expected, in the CEMIB pathogen-free animals. As the animals maintained in a conventional animal facility developed a very discrete clinical, and histopathological EAE in comparison to the rats kept in pathogen-free conditions, we believe that environmental factors such as intestinal parasites could underlie this resistance to EAE development, supporting the applicability of the hygiene hypothesis to EAE.     

Soil carbon storage and nitrogen and phosphorous availability in loblolly pine plantations over 4 to16 years of herbicide and fertilizer treatments

The impact of extended herbicide (H) and annual fertilizer (F) treatments on the mineral soil carbon (C) pool and nitrogen (N) and phosphorous (P) availability were analyzed in managed loblolly pine (Pinus taeda L.) plantations in the Piedmont of Georgia in stands ranging from 4 to 16 years old. Mineral soil C, N, P, and extractable P were measured in 66 plots in three locations comparing H, F, and their combination HF to the Control plots. Soils were sampled in January 2000 near Eatonton (n = 40), in August 2001 near Athens (n = 12), and in March 2003 near Dawsonville (n = 14). In addition, twelve plots (two H and two HF at each location) were measured on 17 dates using a mixed bead resin core technique to estimate mineral soil N availability. At all three study locations the H treatment tended to deplete the mineral soil C pool while, overall, the F treatments did not determine any significant mineral soil C increase. The soil C pool (0- to 50-cm depth) was depleted by about 5 Mg C ha⁻¹ under the H-treated plots near Eatonton. The HF plots had much higher resin-extractable N than the corresponding H plots in all months of the year. At a plot level, HF values ranged from about 9 to 3,195 μg N g⁻¹ resin while H values ranged from about 4 to 858 μg N g⁻¹ resin. The corresponding annual cumulative resin-extractable N ranged from about 13 kg N ha⁻¹ in the H to about 372 kg N ha⁻¹ in the HF. Extractable P values were also elevated in all F-treated plots. Fertilization and herbicide treatments favored C sequestration only in the aboveground biomass. No significant change was observed in the mineral soil C pool, despite the generally observed increases in soil available N and P.     

Status of the enigmatic Oriental genus Rhithrogeniella Ulmer, 1939 (Ephemeroptera,Heptageniidae)

Based on historic collections and new material from Sumatra and Java, the species Rhithrogeniella ornata Ulmer, 1939, type species of the genus Rhithrogeniella, is reinvestigated. The nymph is described for the first time and is closely related to the continental Southeast Asian species Rhithrogeniella tonkinensis Soldán and Braasch, 1986. Rhithrogeniella belongs to the subfamily Ecdyonurinae, and is related to the genera Nixe Flowers, 1980 and/or Paracinygmula Bajkova, 1975 based on characters of the nymphal stage. Species described from Taiwan in the genus Nixe are transferred to the genus Rhithrogeniella: Rh. littoralis (Kang and Yang, 1994) comb. n., Rh. mitifica (Kang and Yang, 1994) comb. n. and Rh. obscura (Kang and Yang, 1994) comb. n.     

Controlled intramyocardial release of engineered chemokines by biodegradable hydrogels as a treatment approach of myocardial infarction

Myocardial infarction (MI) induces a complex inflammatory immune response, followed by the remodelling of the heart muscle and scar formation. The rapid regeneration of the blood vessel network system by the attraction of hematopoietic stem cells is beneficial for heart function. Despite the important role of chemokines in these processes, their use in clinical practice has so far been limited by their limited availability over a long time‐span in vivo. Here, a method is presented to increase physiological availability of chemokines at the site of injury over a defined time‐span and simultaneously control their release using biodegradable hydrogels. Two different biodegradable hydrogels were implemented, a fast degradable hydrogel (FDH) for delivering Met‐CCL5 over 24 hrs and a slow degradable hydrogel (SDH) for a gradual release of protease‐resistant CXCL12 (S4V) over 4 weeks. We demonstrate that the time‐controlled release using Met‐CCL5‐FDH and CXCL12 (S4V)‐SDH suppressed initial neutrophil infiltration, promoted neovascularization and reduced apoptosis in the infarcted myocardium. Thus, we were able to significantly preserve the cardiac function after MI. This study demonstrates that time‐controlled, biopolymer‐mediated delivery of chemokines represents a novel and feasible strategy to support the endogenous reparatory mechanisms after MI and may compliment cell‐based therapies.     

Identification of Optimal Reference Genes for Gene Expression Normalization in a Wide Cohort of Endometrioid Endometrial Carcinoma Tissues

Accurate normalization is a primary component of a reliable gene expression analysis based on qRT-PCR technique. While the use of one or more reference genes as internal controls is commonly accepted as the most appropriate normalization strategy, many qPCR-based published studies still contain data poorly normalized and reference genes arbitrarily chosen irrespective of the particular tissue and the specific experimental design. To date, no validated reference genes have been identified for endometrial cancer tissues. In this study, 10 normalization genes (GAPDH, B2M, ACTB, POLR2A, UBC, PPIA, HPRT1, GUSB, TBP, H3F3A) belonging to different functional and abundance classes in various tissues and used in different studies, were analyzed to determine their applicability. In total, 100 endometrioid endometrial cancer samples, which were carefully balanced according to their tumor grade, and 29 normal endometrial tissues were examined using SYBR Green Real-Time RT-PCR. The expression stability of candidate reference genes was determined and compared by means of geNorm and NormFinder softwares. Both algorithms were in agreement in identifying GAPDH, H3F3A, PPIA, and HPRT1 as the most stably expressed genes, only differing in their ranking order. Analysis performed on the expression levels of all candidate genes confirm HPRT1 and PPIA as the most stably expressed in the study groups regardless of sample type, to be used alone or better in combination. As the stable expression of HPRT1 and PPIA between normal and tumor endometrial samples fulfill the basic requirement of a reference gene to be used for normalization purposes, HPRT1 expression showed significant differences between samples from low-grade and high-grade tumors. In conclusion, our results recommend the use of PPIA as a single reference gene to be considered for improved reliability of normalization in gene expression studies involving endometrial tumor samples at different tumor degrees.