The effect of prime-site occupancy on the hepatitis C virus NS3 protease structure.

We recently reported a new class of inhibitors of the chymotrypsin-like serine protease NS3 of the hepatitis C virus. These inhibitors exploit the binding potential of the S′ site of the protease, which is not generally used by the natural substrates. The effect of prime-site occupancy was analyzed by circular dichroism spectroscopy and limited proteolysis-mass spectrometry. Generally, nonprime inhibitors cause a structural change in NS3. Binding in the S′ site produces additional conformational changes with different binding modes, even in the case of the NS3/4A cofactor complex. Notably, inhibitor binding either in the S or S′ site also has profound effects on the stabilization of the protease. In addition, the stabilization propagates to regions not in direct contact with the inhibitor. In particular, the N-terminal region, which according to structural studies is endowed with low structural stability and is not stabilized by nonprime inhibitors, was now fully protected from proteolytic degradation. From the perspective of drug design, P-P′ inhibitors take advantage of binding pockets, which are not exploited by the natural HCV substrates; hence, they are an entry point for a novel class of NS3/4A inhibitors. Here we show that binding of each inhibitor is associated with a specific structural rearrangement. The development of a range of inhibitors belonging to different classes and an understanding of their interactions with the protease are required to address the issue of the most likely outcome of viral protease inhibitor therapy, that is, viral resistanc

Development of personalized thrombogenesis and thrombin generation assays to assess endothelial dysfunction in cardiovascular diseases

The study of endothelial dysfunction (ED) is crucial to identify the pathogenetic mechanism(s) and provide indications for patient management in cardiovascular diseases. It is currently hindered by the limited availability of patient-specific primary endothelial cells (ECs). Endothelial colony-forming cells (ECFCs) represent an optimal non-invasive tool to overcome this issue. Therefore, we investigated the use of ECFCs as a substrate in thrombogenesis and thrombin generation assay (TGA) to assess ED. Both assays were set up on human umbilical vein endothelial cells (HUVECs) and then tested on ECFCs obtained from healthy donors. To prove the ability of the assays to detect endothelial activation, ECs stimulated with TNFα were compared with unstimulated ECs. EC activation was confirmed by the upregulation of VCAM-1 and Tissue Factor expression. Both assays discriminated between unstimulated and activated HUVECs and ECFCs, as significantly higher platelet deposition and fibrin formation in thrombogenesis assay, and thrombin generation in TGA, were observed when TNFα-activated ECs were used as a substrate. The amount of fibrin and thrombin measured in the two assays were directly correlated. Our results support the combined use of a thrombogenesis assay and TGA performed on patient-derived ECFCs to provide a personalized global assessment of ED relevant to the patient’s hemostatic profile

Increased tooth brushing frequency is associated with reduced gingival pocket bacterial diversity in patients with intracranial aneurysms

Objectives The objective of this study was to investigate the association of tooth brushing frequency and bacterial communities of gingival crevicular fluid in patients subjected to preoperative dental examination prior to operative treatment for unruptured intracranial aneurysms. Methods Gingival crevicular fluid samples were taken from their deepest gingival pocket from a series of hospitalized neurosurgical patients undergoing preoperative dental screening (n = 60). The patients were asked whether they brushed their teeth two times a day, once a day, or less than every day. Total bacterial DNA was isolated and the V3–V4 region of the 16S rRNA gene was amplificated. Sequencing was performed with Illumina’s 16S metagenomic sequencing library preparation protocol and data were analyzed with QIIME (1.9.1) and R statistical software (3.3.2). Results Bacterial diversity (Chao1 index) in the crevicular fluid reduced along with reported tooth brushing frequency (p = 0.0002; R2 = 34%; p (adjusted with age and sex) = 0.09; R2 = 11%) showing that patients who reported brushing their teeth twice a day had the lowest bacterial diversity. According to the differential abundant analysis between the tooth brushing groups, tooth brushing associated with two phyla of fusobacteria [p = 0.0001; p = 0.0007], and one bacteroidetes (p = 0.004) by reducing their amounts. Conclusions Tooth brushing may reduce the gingival bacterial diversity and the abundance of periodontal bacteria maintaining oral health and preventing periodontitis, and thus it is highly recommended for neurosurgical patients

Patterns in airborne pollen and other primary biological aerosol particles (PBAP), and their contribution to aerosol mass and number in a boreal forest

We studied variation in concentrations of airborne pollen and other particles of biological origin in a boreal forest in Finland during 2003–2004. The highest concentrations of pollen were observed in late spring and early summer, whereas the peak concentrations of other particles of biological origin (including e.g. fungal spores) occurred in August–September. Although the patterns in concentrations in 2003 and 2004 were similar, the concentration levels were significantly different between the years. The contribution of pollen and other particles of biological origin led to an increase in the measured particulate matter (PM) mass during the pollen season (mass of pollen and other particles of biological origin 5.9 and 0.4 μg m–3, respectively, in respect to PMtotal mass of 9.9 μg m–3) but the effect on total particle number was negligible. The other particles of biological origin constituted the largest fraction of measured primary biological aerosol particle (PBAP) numbers (~99%), whereas pollen showed a higher relative mass fraction (~97%) of PBAP. These results underline the important contribution of PBAP to coarse atmospheric particle mass providing up to 65% of the total mass during the peak pollen season

5-fluorouracil modulated by leucovorin, methotrexate and mitomycin: highly effective, low-cost chemotherapy for advanced colorectal cancer

We have reported that an alternating regimen of bolus and continuous infusion 5-fluorouracil (FU) was superior to bolus FU in terms of response rate and progression-free survival in advanced colorectal cancer. Biochemical modulation was an essential part of this regimen and it was selective for the schedule of FU administration: bolus FU was in fact modulated by methotrexate (MTX) while continuous infusion FU was potentiated by 6-s-leucovorin (LV). Considering the low cost and the favourable report on the activity of mitomycin C (mito) added to CI FU, we have incorporated this agent in the infusional part of our treatment programme. 105 patients with untreated, advanced, measurable colorectal cancer were accrued from 13 Italian centres and treated with the following regimen. 2 biweekly cycles of FU bolus (600 mg/m2), modulated by MTX (24 h earlier, 200 mg/m2) were alternated with a 3-week continuous infusion of FU (200 mg/m2daily), modulated by LV (20 mg/m2weekly bolus). Mito, 7 mg/m2, was given on the first day of the infusional period. After a 1 week rest, the whole cycle (8 weeks) was repeated, if indicated. 5 complete and 34 partial responses were obtained (response rate, 37% on the intention to treat basis; 95% confidence limits, 28–46%). After a median follow-up time of 26 months, 37 patients are still alive. The median progression-free survival is 7.7 months with an overall survival of 18.8 months and a 2-year survival rate of 30%. The regimen was very well tolerated with fewer than 13% of patients experiencing WHO grade III–IV toxicity. These results are consistent with those obtained by our group in 3 previous trials of schedule specific biochemical modulation of FU. They also indicate a highly active, little toxic, inexpensive regimen of old drugs to be used (a) as an alternative to the more expensive combinations including CPT-11 or oxaliplatin or (b) as the basis for combination programmes with these agents. © 2001 Cancer Research Campaign http://www.bjcancer.co

Type II supernovae from the Carnegie Supernova Project-I. I. Bolometric light curves of 74 SNe II using uBgVriYJH photometry

The present study is the first of a series of three papers where we characterise the type II supernovae (SNe~II) from the Carnegie Supernova Project-I to understand their diversity in terms of progenitor and explosion properties. In this first paper, we present bolometric light curves of 74 SNe~II. We outline our methodology to calculate the bolometric luminosity, which consists of the integration of the observed fluxes in numerous photometric bands ($uBgVriYJH$) and black-body (BB) extrapolations to account for the unobserved flux at shorter and longer wavelengths. BB fits were performed using all available broadband data except when line blanketing effects appeared. Photometric bands bluer than $r$ that are affected by line blanketing were removed from the fit, which makes near-infrared (NIR) observations highly important to estimate reliable BB extrapolations to the infrared. BB fits without NIR data produce notably different bolometric light curves, and therefore different estimates of SN~II progenitor and explosion properties when data are modelled. We present two methods to address the absence of NIR observations: (a) colour-colour relationships from which NIR magnitudes can be estimated using optical colours, and (b) new prescriptions for bolometric corrections as a function of observed SN~II colours. Using our 74 SN~II bolometric light curves, we provide a full characterisation of their properties based on several observed parameters. We measured magnitudes at different epochs, as well as durations and decline rates of different phases of the evolution. An analysis of the light-curve parameter distributions was performed, finding a wide range and a continuous sequence of observed parameters which is consistent with previous analyses using optical light curves.Comment: Accepted for publication in A&

Type II supernovae from the Carnegie Supernova Project-I. II. Physical parameter distributions from hydrodynamical modelling

Linking supernovae to their progenitors is a powerful method for furthering our understanding of the physical origin of their observed differences, while at the same time testing stellar evolution theory. In this second study of a series of three papers where we characterise SNe II to understand their diversity, we derive progenitor properties (initial and ejecta masses, and radius), explosion energy, $^{56}$Ni mass, and its degree of mixing within the ejecta for a large sample of SNe II. This dataset was obtained by the Carnegie Supernova Project-I and is characterised by a high cadence of their optical and NIR light curves and optical spectra that were homogeneously observed and processed. A large grid of hydrodynamical models and a fitting procedure based on MCMC methods were used to fit the bolometric light curve and the evolution of the photospheric velocity of 53 SNe II. We infer ejecta masses between 7.9 and 14.8 $M_{\odot}$, explosion energies between 0.15 and 1.40 foe, and $^{56}$Ni masses between 0.006 and 0.069 $M_{\odot}$. We define a subset of 24~SNe (the `gold sample') with well-sampled bolometric light curves and expansion velocities for which we consider the results more robust. Most SNe~II in the gold sample ($\sim$88%) are found with ejecta masses in the range of $\sim$8-10 $M_{\odot}$, coming from low zero-age main-sequence masses (9-12 $M_{\odot}$). The modelling of the initial-mass distribution of the gold sample gives an upper mass limit of 21.3$^{+3.8}_{-0.4}$ $M_{\odot}$ and a much steeper distribution than that for a Salpeter massive-star IMF. This IMF incompatibility is due to the large number of low-mass progenitors found -- when assuming standard stellar evolution. This may imply that high-mass progenitors lose more mass during their lives than predicted. However, a deeper analysis of all stellar evolution assumptions is required to test this hypothesis.Comment: Accepted for publication in Astronomy & Astrophysic

Type II supernovae from the Carnegie Supernova Project-I: I. Bolometric light curves of 74 SNe II using uBgVriYJH photometry

The present study is the first of a series of three papers where we characterise the type II supernovae (SNe II) from the Carnegie Supernova Project-I to understand their diversity in terms of progenitor and explosion properties. In this first paper, we present bolometric light curves of 74 SNe II. We outline our methodology to calculate the bolometric luminosity, which consists of the integration of the observed fluxes in numerous photometric bands (uBgVriYJH) and black-body (BB) extrapolations to account for the unobserved flux at shorter and longer wavelengths. BB fits were performed using all available broadband data except when line blanketing effects appeared. Photometric bands bluer than r that are affected by line blanketing were removed from the fit, which makes near-infrared (NIR) observations highly important to estimate reliable BB extrapolations to the infrared. BB fits without NIR data produce notably different bolometric light curves, and therefore different estimates of SN II progenitor and explosion properties when data are modelled. We present two methods to address the absence of NIR observations: (a) colour-colour relationships from which NIR magnitudes can be estimated using optical colours, and (b) new prescriptions for bolometric corrections as a function of observed SN II colours. Using our 74 SN II bolometric light curves, we provide a full characterisation of their properties based on several observed parameters. We measured magnitudes at different epochs, as well as durations and decline rates of different phases of the evolution. An analysis of the light-curve parameter distributions was performed, finding a wide range and a continuous sequence of observed parameters which is consistent with previous analyses using optical light curves.The work of the Carnegie Supernova Project was supported by the National Science Foundation under grants AST-0306969, AST-0607438, AST-1008343, AST-1613426, AST-1613472, and AST-1613455. L. M. acknowledges support from a CONICET fellowship. L. M. and M. O. acknowledge support from UNRN PI2018 40B885 grant. M. H. acknowledges support from the Hagler Institute of Advanced Study at Texas A&M University. S. G. G. acknowledges support by FCT under Project CRISP PTDC/FIS-AST-31546/2017 and Project No. UIDB/00099/2020. M. S. is supported by grants from the VILLUM FONDEN (grant number 28021) and the Independent Research Fund Denmark (IRFD; 8021-00170B). F. F. acknowledges support from the National Agency for Research and Development (ANID) grants: BASAL Center of Mathematical Modelling AFB-170001, Ministry of Economy, Development, and Tourism’s Millennium Science Initiative through grant IC12009, awarded to the Millennium Institute of Astrophysics, and FONDECYT Regular #1200710. L. G. acknowledges financial support from the Spanish Ministry of Science, Innovation and Universities (MICIU) under the 2019 Ramón y Cajal program RYC2019-027683 and from the Spanish MICIU project PID2020-115253GA-I00. P.H. acknowledges the support by National Science Foundation (NSF) grant AST-1715133

Comparison of the optical light curves of hydrogen-rich and hydrogen-poor type II supernovae

Type II supernovae (SNe II) show strong hydrogen features in their spectra throughout their whole evolution, while type IIb supernovae (SNe IIb) spectra evolve from dominant hydrogen lines at early times to increasingly strong helium features later on. However, it is currently unclear whether the progenitors of these SN types form a continuum in pre-SN hydrogen mass or whether they are physically distinct. SN light-curve morphology directly relates to progenitor and explosion properties such as the amount of hydrogen in the envelope, the pre-SN radius, the explosion energy, and the synthesized mass of radioactive material. In this work, we study the morphology of the optical-wavelength light curves of hydrogen-rich SNe II and hydrogen-poor SNe IIb to test whether an observational continuum exists between the two. Using a sample of 95 SNe (73 SNe II and 22 SNe IIb), we define a range of key observational parameters and present a comparative analysis between both types. We find a lack of events that bridge the observed properties of SNe II and IIb. Light-curve parameters such as rise times and post-maximum decline rates and curvatures clearly separate both SN types and we therefore conclude that there is no continuum, with the two SN types forming two observationally distinct families. In the V band a rise time of 17 d (SNe II lower and SNe IIb higher), and a magnitude difference between 30 and 40 d post-explosion of 0.4 mag (SNe II lower and SNe IIb higher) serve as approximate thresholds to differentiate both types.Fil: Pessi, Priscila Jael. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Astrofísica La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas. Instituto de Astrofísica La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas; ArgentinaFil: Folatelli, Gaston. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Astrofísica La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas. Instituto de Astrofísica La Plata; ArgentinaFil: Anderson, J. P.. European Southern Observatory Chile.; ChileFil: Bersten, Melina Cecilia. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Astrofísica La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas. Instituto de Astrofísica La Plata; ArgentinaFil: Burns, C.. Observatories Of The Carnegie Institution For Science; Estados UnidosFil: Contreras, C.. Las Campanas Observatory; Chile. Space Telescope Science Institute; Estados UnidosFil: Davis, S.. Florida State University; Estados UnidosFil: Englert Urrutia, Brenda Nahir. Ministerio de Ciencia. Tecnología e Innovación Productiva. Agencia Nacional de Promoción Científica y Tecnológica; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas; ArgentinaFil: Hamuy, M.. Universidad de Chile; ChileFil: Hsiao, Eric. Florida State University; Estados UnidosFil: Martinez, Laureano. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Astrofísica La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas. Instituto de Astrofísica La Plata; ArgentinaFil: Morrell, Nidia Irene. Las Campanas Observatory; Chile. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Astrofísica La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas. Instituto de Astrofísica La Plata; ArgentinaFil: Phillips, M. M.. Las Campanas Observatory; ChileFil: Suntzeff, N.. Texas A&M University; Estados UnidosFil: Stritzinger, M. D.. University Aarhus; Dinamarc