Targeting the Essential Transcription Factor HP1043 of Helicobacter pylori: A Drug Repositioning Study

Antibiotic-resistant bacterial pathogens are a very challenging problem nowadays. Helicobacter pylori is one of the most widespread and successful human pathogens since it colonizes half of the world population causing chronic and atrophic gastritis, peptic ulcer, mucosa-associated lymphoid tissue-lymphoma, and even gastric adenocarcinoma. Moreover, it displays resistance to numerous antibiotics. One of the H. pylori pivotal transcription factors, HP1043, plays a fundamental role in regulating essential cellular processes. Like other bacterial transcription factors, HP1043 does not display a eukaryote homolog. These characteristics make HP1043 a promising candidate to develop novel antibacterial strategies. Drug repositioning is a relatively recent strategy employed in drug development; testing approved drugs on new targets considerably reduces the time and cost of this process. The combined computational and in vitro approach further reduces the number of compounds to be tested in vivo. Our aim was to identify a subset of known drugs able to prevent HP1043 binding to DNA promoters. This result was reached through evaluation by molecular docking the binding capacity of about 14,350 molecules on the HP1043 dimer in both conformations, bound and unbound to the DNA. Employing an ad hoc pipeline including MMGBSA molecular dynamics, a selection of seven drugs was obtained. These were tested in vitro by electrophoretic mobility shift assay to evaluate the HP1043–DNA interaction. Among these, three returned promising results showing an appreciable reduction of the DNA-binding activity of HP1043. Overall, we applied a computational methodology coupled with experimental validation of the results to screen a large number of known drugs on one of the H. pylori essential transcription factors. This methodology allowed a rapid reduction of the number of drugs to be tested, and the drug repositioning approach considerably reduced the drug design costs. Identified drugs do not belong to the same pharmaceutical category and, by computational analysis, bound different cavities, but all display a reduction of HP1043 binding activity on the DNA

Visual Tools for a Multiple Cross-reading in the Exhibition Context

As researchers who participate in common studies, we need a tool for reading and understanding collected data in its complexity, for analysing and researching the relationship between records at various levels of information within the database, and for getting them networked. This paper presents our project for a visual tool characterized by an interface based on an interactive system for data visualization, which can be configured as required. Graphs and diagrams become part of the process and tools for verifying and enhancing the state of the research

appraisal of clinical complications after 23 827 oocyte retrievals in a large assisted reproductive technology program

Objective To assess complications encountered after transvaginal oocyte retrieval procedures. Design Retrospective analysis. Setting University hospital, fertility center. Patient(s) A total of 23,827 consecutive transvaginal oocyte retrieval procedures in 12,615 patients. Intervention(s) Oocyte retrieval procedures performed between June 1996 and October 2016. Main Outcome Measure(s) All oocyte retrieval complications. Those requiring hospital admission for at least 24 hours were considered severe. Result(s) A total of 96 patients (0.76 %) suffered complications, with hospital admission necessary for 71 patients (0.56 %). When calculated per retrieval, the overall complication rate was 0.4%, whereas 0.29% was the admission rate, with an average duration of hospital stay of 2.77 ± 2.5 days. A surgical procedure was necessary for 24 patients (0.1% per retrieval and 0.19% per patient). Multivariate analysis showed a significant correlation between complications and women age, body mass index (BMI), the number oocyte retrieved, and the mean time to complete oocyte retrieval. The incidence of complications was significantly higher for physicians who had performed 250 retrievals (odds ratio 0.63, 95% confidence interval 0.40–0.99). Conclusion(s) Oocyte retrieval can be considered a safe procedure but is not without risks. The most important, identifiable, risk factors for the occurrence of complications are: [1] high number of oocytes retrieved, [2] a long duration of the procedure and mean time per oocyte retrieved, [3] inexperience of the surgeon, [4] younger patients with a lesser BMI, and [5] history of prior abdominal or pelvic surgery or pelvic inflammatory disease. Clinical Trial Registration Number NCT03282279

The actinomycete Kitasatospora sp. SeTe27, subjected to adaptive laboratory evolution (ALE) in the presence of selenite, varies its cellular morphology, redox stability, and tolerance to the toxic oxyanion

The effects of oxyanions selenite (SeO32−) in soils are of high concern in ecotoxicology and microbiology as they can react with mineral particles and microorganisms. This study investigated the evolution of the actinomycete Kitasatospora sp. SeTe27 in response to selenite. To this aim, we used the Adaptive Laboratory Evolution (ALE) technique, an experimental approach that mimics natural evolution and enhances microbial fitness for specific growth conditions. The original strain (wild type; WT) isolated from uncontaminated soil gave us a unique model system as it has never encountered the oxidative damage generated by the prooxidant nature of selenite. The WT strain exhibited a good basal level of selenite tolerance, although its growth and oxyanion removal capacity were limited compared to other environmental isolates. Based on these premises, the WT and the ALE strains, the latter isolated at the end of the laboratory evolution procedure, were compared. While both bacterial strains had similar fatty acid profiles, only WT cells exhibited hyphae aggregation and extensively produced membrane-like vesicles when grown in the presence of selenite (challenged conditions). Conversely, ALE selenite-grown cells showed morphological adaptation responses similar to the WT strain under unchallenged conditions, demonstrating the ALE strain improved resilience against selenite toxicity. Whole-genome sequencing revealed specific missense mutations in genes associated with anion transport and primary and secondary metabolisms in the ALE variant. These results were interpreted to show that some energy-demanding processes are attenuated in the ALE strain, prioritizing selenite bioprocessing to guarantee cell survival in the presence of selenite. The present study indicates some crucial points for adapting Kitasatospora sp. SeTe27 to selenite oxidative stress to best deal with selenium pollution. Moreover, the importance of exploring non-conventional bacterial genera, like Kitasatospora, for biotechnological applications is emphasized

Neoangiogenesis markers in canine urothelial carcinomas: A cross‐sectional study

Background: In humans, there is a growing body of evidence that neoangiogenesis is crucial for tumour growth and progression in urothelial carcinomas (UC) which also typically exhibit overactivation of the RAS-MAPK pathway. In canine UC (cUC), the same pathway has been aberrantly activated due to V595E BRAF variant and BRAF inhibitors has been evaluated as more effective treatment. However, BRAF inhibition is hampered in humans by rapidly occurring of chemoresistance. Targeting angiogenesis has been speculated to increase the effectiveness of BRAF inhibitors and to delay the development of chemoresistance. Objectives: This study aimed to investigate the level of angiogenic markers in urine samples of UC affected dogs (n = 15) in comparison to an unmatched control group (n = 16) along with the clinical, morphological and molecular features. Methods: In urine, both vascular endothelial growth factor (VEGF) concentration, using an ELISA assay, and MMP2 and 9 activities, using the zymographic assay, were measured. BRAF analysis was carried out using a digital PCR method. Results: Urinary VEGF concentration (mean pg/g_uCrea 6.9 +/- 27.7 vs. 1074 +/- 1797, p < 0.01) and MMP activity (mean 6.8 x 10(6) +/- 9.2 x 10(6) vs. 2.5 x 10(7) +/- 2.3 x 10(7), p < 0.05) were higher in affected dogs than in healthy controls. Urinary active MMP9 was significantly correlated with T3 stage, it was absent in dogs with undetectable VEGF and it correlated well with urinary VEGF concentration. In this cohort, 10/10 UC affected dogs exhibited the V595E BRAF variation. Conclusion: The findings are consistent with the presence of overactive neoangiogenesis in cUC. Urinary active MMP9 may be suitable for use as tumour progression biomarker. The addition of angiogenesis targeting may be rationale for novel therapeutic strategies

Fast Liquid Chromatography Coupled with Tandem Mass Spectrometry for the Analysis of Vanillic and Syringic Acids in Ice Cores

The development of new analytical systems and the improvement of the existing ones to obtain high-resolution measurements of chemical markers in samples from ice cores, is one of the main challenges the paleoclimatic scientific community is facing. Different chemical species can be used as markers for tracking emission sources or specific environmental processes. Although some markers, such as methane sulfonic acid (a proxy of marine productivity), are commonly used, there is a lack of data on other organic tracers in ice cores, making their continuous analysis analytically challenging. Here, we present an innovative combination of fast liquid chromatography coupled with tandem mass spectrometry (FLC-MS/MS) to continuously determine organic markers in ice cores. After specific optimization, this approach was applied to the quantification of vanillic and syringic acids, two specific markers for biomass burning. Using the validated method, detection limits of 3.6 and 4.6 pg mL–1 for vanillic and syringic acids, respectively, were achieved. Thanks to the coupling of FLC-MS/MS with the continuous flow analytical system, we obtained one measurement every 30 s, which corresponds to a sampling resolution of a sample every 1.5 cm with a melting rate of 3.0 cm min–1. To check the robustness of the method, we analyzed two parallel sticks of an alpine ice core over more than 5 h. Vanillic acid was found with concentrations in the range of picograms per milliliter, suggesting the combustion of coniferous trees, which are found throughout the Italian Alps.publishedVersio

An Observational Retrospective Cohort Trial on 4,828 IVF Cycles Evaluating Different Low Prognosis Patients Following the POSEIDON Criteria

Objective: To study the actual controlled ovarian stimulation (COS) management in women with suboptimal response, comparing clinical outcomes to the gonadotropins consume, considering potential role of luteinizing hormone (LH) addition to follicle-stimulating hormone (FSH).Design: Monocentric, observational, retrospective, real-world, clinical trial on fresh intra-cytoplasmic sperm injection (ICSI) cycles retrieving from 1 to 9 oocytes, performed at Humanitas Fertility Center from January 1st, 2012 to December 31st, 2015.Methods: COS protocols provided gonadotropin releasing-hormone (GnRH) agonist long, flare-up, short and antagonist. Both recombinant and urinary FSH were used for COS and LH was added according to the clinical practice. ICSI outcomes considered were: gonadotropins dosages; total, mature, injected and frozen oocytes; cumulative, transferred and frozen embryos; implantation rate; pregnancy, delivery and miscarriage rates. Outcomes were compared according to the gonadotropin regimen used during COS.Results: Our cohort showed 20.8% of low responders, defined as 1-3 oocytes retrieved and 79.2% of "suboptimal" responders, defined as 4-9 oocytes retrieved. According to recent POSEIDON stratification, cycles were divided in group 1 (6.9%), 2 (19.8%), 3 (11.7%), and 4 (61.5%). The cohort was divided in 3 groups, according to the gonadotropin's regimen. Women treated with FSH plus LH showed worst prognostic factors, in terms of age, basal FSH, AMH, and AFC. This difference was evident in suboptimal responders, whereas only AMH and AFC were different among treatment groups in low responders. Although a different result, in terms of oocytes and embryos detected, major ICSI outcomes (i.e., pregnancy and delivery rates) were similar among groups of COS treatment. Outcomes were significantly different among Poseidon groups. Implantation, pregnancy and delivery rates were significantly higher in Poseidon group 1 and progressively declined in other POSEIDON groups, reaching the worst percentage in group 4.Conclusions: In clinical practice, women with worst prognosis factors are generally treated with a combination of LH and FSH. Despite low prognosis women showed a reduced number of oocytes retrieved, the final ICSI outcome, in terms of pregnancy, is similarly among treatment group. This result suggests that the LH addition to FSH during COS could improve the quality of oocytes retrieved, balancing those differences that are evident at baseline

An upgraded CFA - FLC - MS/MS system for the semi-continuous detection of levoglucosan in ice cores

A new Continuous Flow Analysis (CFA) system coupled with Fast Liquid Chromatography – tandem Mass Spectrometry (FLC-MS/MS) has been recently developed for determining organic markers in ice cores. In this work we present an upgrade of this innovative technique, optimized for the detection of levoglucosan in ice cores, a crucial tracer for reconstructing past fires. The upgrade involved a specific optimization of the chromatographic and mass spectrometric parameters, allowing for a higher sampling resolution (down to 1 cm) and the simultaneous collection of discrete samples, for off-line analysis of water stable isotopes and additional chemical markers. The robustness and repeatability of the method has been tested by the analysis of multiple sticks of ice cut from the same shallow alpine ice core, and running the system for several hours on different days. The results show similar and comparable trends between the ice sticks. With this upgraded system, a higher sensitivity and a lower limit of detection (LOD) was achieved compared to discrete analysis of alpine samples for levoglucosan measurements. The new LOD was as low as 66 ng L−1, a net improvement over the previous LOD of 600 ng L−1

High kinetic inductance NbTiN films for quantum limited travelling wave parametric amplifiers

A wide-bandwidth and low-noise amplification chain in the microwave regime is crucial for the efficient read-out of quantum systems based on superconducting detectors, such as Microwave Kinetic Inductance Detectors (MKIDs), Transition Edge Sensors (TESs), Magnetic Microcalorimeters (MMCs), and RF cavities, as well as qubits. Kinetic Inductance Travelling Wave Parametric Amplifiers (KI-TWPAs) operated in a three-wave mixing fashion have demonstrated exceptional dynamic range and low-noise performance, approaching the quantum limit. These amplifiers can be fabricated using a single layer of a high kinetic inductance film as weakly dispersive artificial transmission lines, with the ability to control the phase-matched bandwidth through dispersion engineering. In this study, we present the optimisation of the rf sputter-deposition process of NbTiN films using a Nb80%T20 target, with the goal of achieving precise control over film characteristics, resulting in high kinetic inductance while maintaining a high transition temperature. The parameter landscape related to the different sputtering conditions, such as pressure, power, and nitrogen flow, has been explored and the film thickness has been used as a fine-tuning parameter to adjust the properties of the final NbTiN films used for the fabrication of KI-TWPAs. As a final result, we have obtained a NbTiN film with a kinetic inductance of 8.5 pH/sq which we have exploited to fabricate KI-TWPA prototype devices, showing promising amplification performance

Long-Term Outcome After Adoptive Immunotherapy With Natural Killer Cells: Alloreactive NK Cell Dose Still Matters

Recently, many reports were published supporting the clinical use of adoptivelytransferred natural killer (NK) cells as a therapeutic tool against cancer, including acutemyeloid leukemia (AML). Our group demonstrated promising clinical response usingadoptive immunotherapy with donor-derived alloreactive KIR-ligand-mismatched NK cellsin AML patients. Moreover, the antileukemic effect was correlated with the dose of infusedalloreactive NK cells (“functional NK cell dose”). Herein, we update the results of ourprevious study on a cohort of adult AML patients (median age at enrollment 64) infirstmorphological complete remission (CR), not eligible for allogeneic stem celltransplantation. After an extended median follow-up of 55.5 months, 8/16 evaluablepatients (50%) are still off-therapy and alive disease-free. Overall survival (OS) and disease-free survival (DFS) are related with the dose of infused alloreactive NK cells (≥2×105/kg