Modified PNA design and synthesis: a novel approach using Molecular Dynamics and Metadynamics

Gli acidi peptido nucleici sono potenti strumenti utilizzati in ambito biotecnologico per colpire DNA o RNA. PNA contenenti basi o backbone modificati sono attualmente studiati per migliorarne le proprietà in ambito biologico. Bersagliare i micro RNA (anti-miR) è particolarmente interessante nell’ottica di future applicazioni terapeutiche, ma strumenti computazionali che aiutino nel design di nuovi PNA anti-miR non sono stati ancora completamente sviluppati. Le proprietà conformazionali del singolo filamento di PNA (non modificato o recante modificazioni in γ) e dei duplex PNA:RNA e i processi di re-annealing e melting sono stati studiati tramite Dinamica Molecolare e Metadinamica. L’approccio computazionale consolidato, assieme a un programma modificato per la generazione delle strutture dei duplex contenenti PNA, è stato utilizzato per il virtual screening di PNA contenenti basi modificate. Sono state inoltre sintetizzate le unità per l’ottenimento del composto più promettente e una funzione idrolitica da legare al monomero finale.

The electron-furfural scattering dynamics for 63 energetically open electronic states

We report on integral-, momentum transfer-and differential cross sections for elastic and electronically inelastic electron collisions with furfural (C5H4O2). The calculations were performed with two different theoretical methodologies, the Schwinger multichannel method with pseudopotentials (SMCPP) and the independent atom method with screening corrected additivity rule (IAM-SCAR) that now incorporates a further interference (I) term. The SMCPP with N energetically open electronic states (N-open) at either the static-exchange (N-open ch-SE) or the static-exchange-plus-polarisation (N-open ch-SEP) approximation was employed to calculate the scattering amplitudes at impact energies lying between 5 eV and 50 eV, using a channel coupling scheme that ranges from the 1ch-SEP up to the 63ch-SE level of approximation depending on the energy considered. For elastic scattering, we found very good overall agreement at higher energies among our SMCPP cross sections, our IAM-SCAR+I cross sections and the experimental data for furan (a molecule that differs from furfural only by the substitution of a hydrogen atom in furan with an aldehyde functional group). This is a good indication that our elastic cross sections are converged with respect to the multichannel coupling effect for most of the investigated intermediate energies. However, although the present application represents the most sophisticated calculation performed with the SMCPP method thus far, the inelastic cross sections, even for the low lying energy states, are still not completely converged for intermediate and higher energies. We discuss possible reasons leading to this discrepancy and point out what further steps need to be undertaken in order to improve the agreement between the calculated and measured cross sections. (C) 2016 AIP Publishing LLC.

HLA-DP2 binding prediction by molecular dynamics simulations

Major histocompatibility complex (MHC) II proteins bind peptide fragments derived from pathogen antigens and present them at the cell surface for recognition by T cells. MHC proteins are divided into Class I and Class II. Human MHC Class II alleles are grouped into three loci: HLA-DP, HLA-DQ, and HLA-DR. They are involved in many autoimmune diseases. In contrast to HLA-DR and HLA-DQ proteins, the X-ray structure of the HLA-DP2 protein has been solved quite recently. In this study, we have used structure-based molecular dynamics simulation to derive a tool for rapid and accurate virtual screening for the prediction of HLA-DP2-peptide binding. A combinatorial library of 247 peptides was built using the "single amino acid substitution" approach and docked into the HLA-DP2 binding site. The complexes were simulated for 1 ns and the short range interaction energies (Lennard-Jones and Coulumb) were used as binding scores after normalization. The normalized values were collected into quantitative matrices (QMs) and their predictive abilities were validated on a large external test set. The validation shows that the best performing QM consisted of Lennard-Jones energies normalized over all positions for anchor residues only plus cross terms between anchor-residues.

Monitoring of transcriptional dynamics of HIF and NFκB activities

Genetic experiments over the last few decades have identified many regulatory proteins critical for DNA transcription. The dynamics of their transcriptional activities shape the differential expression of the genes they control. Here we describe a simple method, based on the secreted luciferase, to measure the activities of two transcription factors NF?B and HIF. This technique can effectively monitor dynamics of transcriptional events in a population of cells and be up-scaled for high-throughput screening and promoter analysis, making it ideal for data-demanding applications such as mathematical modelling.

Classification of Biomedical Signals using the Dynamics of the False Nearest Neighbours (DFNN) Algorithm

* This study was supported in part by the Natural Sciences and Engineering Research Council of Canada, and by the Gastrointestinal Motility Laboratory (University of Alberta Hospitals) in Edmonton, Alberta, Canada.

SYSTEM DYNAMICS MODELING AS A QUANTITATIVE-QUALITATIVE FRAMEWORK FOR SUSTAINABLE WATER RESOURCES MANAGEMENT: INSIGHTS FOR WATER QUALITY POLICY IN THE GREAT LAKES REGION

Early water resources modeling efforts were aimed mostly at representing hydrologic processes, but the need for interdisciplinary studies has led to increasing complexity and integration of environmental, social, and economic functions. The gradual shift from merely employing engineering-based simulation models to applying more holistic frameworks is an indicator of promising changes in the traditional paradigm for the application of water resources models, supporting more sustainable management decisions. This dissertation contributes to application of a quantitative-qualitative framework for sustainable water resources management using system dynamics simulation, as well as environmental systems analysis techniques to provide insights for water quality management in the Great Lakes basin. The traditional linear thinking paradigm lacks the mental and organizational framework for sustainable development trajectories, and may lead to quick-fix solutions that fail to address key drivers of water resources problems. To facilitate holistic analysis of water resources systems, systems thinking seeks to understand interactions among the subsystems. System dynamics provides a suitable framework for operationalizing systems thinking and its application to water resources problems by offering useful qualitative tools such as causal loop diagrams (CLD), stock-and-flow diagrams (SFD), and system archetypes. The approach provides a high-level quantitative-qualitative modeling framework for "big-picture" understanding of water resources systems, stakeholder participation, policy analysis, and strategic decision making. While quantitative modeling using extensive computer simulations and optimization is still very important and needed for policy screening, qualitative system dynamics models can improve understanding of general trends and the root causes of problems, and thus promote sustainable water resources decision making. Within the system dynamics framework, a growth and underinvestment (G&U) system archetype governing Lake Allegan's eutrophication problem was hypothesized to explain the system's problematic behavior and identify policy leverage points for mitigation. A system dynamics simulation model was developed to characterize the lake's recovery from its hypereutrophic state and assess a number of proposed total maximum daily load (TMDL) reduction policies, including phosphorus load reductions from point sources (PS) and non-point sources (NPS). It was shown that, for a TMDL plan to be effective, it should be considered a component of a continuous sustainability process, which considers the functionality of dynamic feedback relationships between socio-economic growth, land use change, and environmental conditions. Furthermore, a high-level simulation-optimization framework was developed to guide watershed scale BMP implementation in the Kalamazoo watershed. Agricultural BMPs should be given priority in the watershed in order to facilitate cost-efficient attainment of the Lake Allegan's TP concentration target. However, without adequate support policies, agricultural BMP implementation may adversely affect the agricultural producers. Results from a case study of the Maumee River basin show that coordinated BMP implementation across upstream and downstream watersheds can significantly improve cost efficiency of TP load abatement.

Structure-based virtual screening of hypothetical inhibitors of the enzyme longiborneol synthase: a potential target to reduce Fusarium head blight disease.

2016

Newborn Hearing Screening And Early Diagnostic In The Nicu.

The aim was to describe the outcome of neonatal hearing screening (NHS) and audiological diagnosis in neonates in the NICU. The sample was divided into Group I: neonates who underwent NHS in one step and Group II: neonates who underwent a test and retest NHS. NHS procedure was automated auditory brainstem response. NHS was performed in 82.1% of surviving neonates. For GI, referral rate was 18.6% and false-positive was 62.2% (normal hearing in the diagnostic stage). In GII, with retest, referral rate dropped to 4.1% and false-positive to 12.5%. Sensorineural hearing loss was found in 13.2% of infants and conductive in 26.4% of cases. There was one case of auditory neuropathy spectrum (1.9%). Dropout rate in whole process was 21.7% for GI and 24.03% for GII. We concluded that it was not possible to perform universal NHS in the studied sample or, in many cases, to apply it within the first month of life. Retest reduced failure and false-positive rate and did not increase evasion, indicating that it is a recommendable step in NHS programs in the NICU. The incidence of hearing loss was 2.9%, considering sensorineural hearing loss (0.91%), conductive (1.83%) and auditory neuropathy spectrum (0.19%).

[why Does The Prevalence Of Cytopathological Results Of Cervical Cancer Screening Can Vary Significantly Between Two Regions Of Brazil?].

To analyze the prevalence of cervical cytopathological results for the screening of cervical cancer with regard to women's age and time since the last examination in Maceió and Rio de Janeiro, Brazil, among those assisted by the Brazilian Unified Health System. Cervical cytopathological results available in the Information System of Cervical Cancer Screening for the year 2011 were analyzed, corresponding to 206,550 for Rio de Janeiro and 45,243 for Maceió. In Rio de Janeiro, examination at one and two year intervals predominated, while in Maceió examination at one and three year intervals had a higher predominance. Women who underwent cervical smear screening in Maceió were older than those in Rio de Janeiro. The prevalence of invasive squamous cell carcinoma was similar for the two cities, but all the other results presented a higher prevalence in Rio de Janeiro: ASCUS (PR=5.32; 95%CI 4.66-6.07); ASCH (PR=4.27; 95%CI 3.15-5.78); atypical glandular cells (PR=10.02; 95%CI 5.66-17.76); low-grade squamous intraepithelial lesions (PR=6.10; 95%CI 5.27-7.07); high-grade squamous intraepithelial lesions (PR=8.90; 95%CI 6.50-12.18) and adenocarcinoma (PR=3.00; 95%CI 1.21-7.44). The rate of unsatisfactory cervical samples was two times higher in Maceió and that of rejected samples for analysis was five times higher in Maceió when compared to Rio de Janeiro. The prevalence rates of altered cervical cytopathological results was significantly higher in Rio de Janeiro than in Maceió. There is no objective information that may justify this difference. One hypothesis is that there may be a difference in the diagnostic performance of the cervical cancer screening, which could be related to the quality of the Pap smear. Thus, these findings suggest that it would be necessary to perform this evaluation at national level, with emphasis on the performance of cervical cancer screening in order to improve the effectiveness of cervical cancer control.

Mechanical Properties And Fracture Dynamics Of Silicene Membranes.

As graphene has become one of the most important materials, there is renewed interest in other similar structures. One example is silicene, the silicon analogue of graphene. It shares some of the remarkable graphene properties, such as the Dirac cone, but presents some distinct ones, such as a pronounced structural buckling. We have investigated, through density functional based tight-binding (DFTB), as well as reactive molecular dynamics (using ReaxFF), the mechanical properties of suspended single-layer silicene. We calculated the elastic constants, analyzed the fracture patterns and edge reconstructions. We also addressed the stress distributions, unbuckling mechanisms and the fracture dependence on the temperature. We analysed the differences due to distinct edge morphologies, namely zigzag and armchair.

Microbial Lipid Production: Screening With Yeasts Grown On Brazilian Molasses.

Rhodotorula glutinis CCT 2182, Rhodosporidium toruloides CCT 0783, Rhodotorula minuta CCT 1751 and Lipomyces starkeyi DSM 70296 were evaluated for the conversion of sugars from Brazilian molasses into single-cell oil (SCO) feedstock for biodiesel. Pulsed fed-batch fermentations were performed in 1.65 l working volume bioreactors. The maximum specific growth rate (µmax), lipid productivity (Pr) and cellular lipid content were, respectively, 0.23 h(-1), 0.41 g l(-1) h(-1), and 41% for Rsp. toruloides; 0.20 h(-1), 0.27 g l(-1) h(-1), and 36% for Rta. glutinis; 0.115 h(-1), 0.135 g l(-1) h(-1), and 27 % for Rta. minuta; and 0.11 h(-1), 0.13 g l(-1) h(-1), and 32% for L. starkeyi. Based on their microbial lipid productivity, content, and profile, Rsp. toruloides and Rta. glutinis are promising candidates for biodiesel production from Brazilian molasses. All the oils from the yeasts were similar to the composition of plant oils (rapeseed and soybean) and could be used as raw material for biofuels, as well as in food and nutraceutical products.

Screening The Life Cycle Of Schistosoma Mansoni Using High-resolution Mass Spectrometry.

Schistosomiasis is a common tropical disease caused by Schistosoma species Schistosomiasis' pathogenesis is known to vary according to the worms' strain. Moreover, high parasitical virulence is directly related to eggs release and granulomatous inflammation in the host's organs. This virulence might be influenced by different classes of molecules, such as lipids. Therefore, better understanding of the metabolic profile of these organisms is necessary, especially for an increased potential of unraveling strain virulence mechanisms and resistance to existing treatments. In this report, direct-infusion electrospray high-resolution mass spectrometry (ESI(+)-HRMS) along with the lipidomic platform were employed to rapidly characterize and differentiate two Brazilian S. mansoni strains (BH and SE) in three stages of their life cycle: eggs, miracidia and cercariae, with samples from experimental animals (Swiss/SPF mice). Furthermore, urine samples of the infected and uninfected mice were analyzed to assess the possibility of direct diagnosis. All samples were differentiated using multivariate data analysis, PCA, which helped electing markers from distinct lipid classes; phospholipids, diacylglycerols and triacylglycerols, for example, clearly presented different intensities in some stages and strains, as well as in urine samples. This indicates that biochemical characterization of S. mansoni may help narrowing-down the investigation of new therapeutic targets according to strain composition and aggressiveness of disease. Interestingly, lipid profile of infected mice urine varies when compared to control samples, indicating that direct diagnosis of schistosomiasis from urine may be feasible.

Site Specific Spin Dynamics In Bafe2as2: Tuning The Ground State By Orbital Differentiation.

The role of orbital differentiation on the emergence of superconductivity in the Fe-based superconductors remains an open question to the scientific community. In this investigation, we employ a suitable microscopic spin probe technique, namely Electron Spin Resonance (ESR), to investigate this issue on selected chemically substituted BaFe2As2 single crystals. As the spin-density wave (SDW) phase is suppressed, we observe a clear increase of the Fe 3d bands anisotropy along with their localization at the FeAs plane. Such an increase of the planar orbital content is interestingly independent of the chemical substitution responsible for suppressing the SDW phase. As a consequence, the magnetic fluctuations in combination with this particular symmetry of the Fe 3d bands are propitious ingredients for the emergence of superconductivity in this class of materials.

[between The Country And The Laboratory: The Dynamics Of The Production Of Knowledge At The Menopause Outpatients Clinic At Caism, Unicamp.]

This study investigates the practices involved in the production of knowledge about menopause at Caism, Unicamp, a reference center for public policies for women's health. Gynecological appointments and psychological support meetings were observed, and women and doctors were interviewed in order to identify what discourse circulates there and how different actors are brought in to ensure that the knowledge produced attains credibility and travels beyond the boundaries of the teaching hospital to become universal. The analysis is based on localized studies aligned with social studies of science and technology.

[between The Country And The Laboratory: The Dynamics Of The Production Of Knowledge At The Menopause Outpatients Clinic At Caism, Unicamp].

This study investigates the practices involved in the production of knowledge about menopause at Caism, Unicamp, a reference center for public policies for women's health. Gynecological appointments and psychological support meetings were observed, and women and doctors were interviewed in order to identify what discourse circulates there and how different actors are brought in to ensure that the knowledge produced attains credibility and travels beyond the boundaries of the teaching hospital to become universal. The analysis is based on localized studies aligned with social studies of science and technology.