Hepatitis C virus (HCV) is a significant public health concern with approximately 160 million people infected worldwide. HCV infection often results in chronic hepatitis, liver cirrhosis and ...hepatocellular carcinoma. No vaccine is available and current therapies are effective against some, but not all, genotypes. HCV is an enveloped virus with two surface glycoproteins (E1 and E2). E2 binds to the host cell through interactions with scavenger receptor class B type I (SR-BI) and CD81, and serves as a target for neutralizing antibodies. Little is known about the molecular mechanism that mediates cell entry and membrane fusion, although E2 is predicted to be a class II viral fusion protein. Here we describe the structure of the E2 core domain in complex with an antigen-binding fragment (Fab) at 2.4 Å resolution. The E2 core has a compact, globular domain structure, consisting mostly of β-strands and random coil with two small α-helices. The strands are arranged in two, perpendicular sheets (A and B), which are held together by an extensive hydrophobic core and disulphide bonds. Sheet A has an IgG-like fold that is commonly found in viral and cellular proteins, whereas sheet B represents a novel fold. Solution-based studies demonstrate that the full-length E2 ectodomain has a similar globular architecture and does not undergo significant conformational or oligomeric rearrangements on exposure to low pH. Thus, the IgG-like fold is the only feature that E2 shares with class II membrane fusion proteins. These results provide unprecedented insights into HCV entry and will assist in developing an HCV vaccine and new inhibitors.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
To estimate minimally important differences (MIDs) on the Functional Assessment of Cancer Therapy–Colorectal (FACT-C) instrument using anchor- and distribution-based methods.
Preliminary MIDs were ...generated for FACT-C scores based on published results for two samples (
n = 60 and
n = 63) from the FACT-C validation study. Preliminary MIDs were confirmed using data from a Phase II randomized controlled clinical trial (
n = 104) and a population-based observational study (
n = 568). MIDs were estimated for the colorectal cancer subscale (CCS); the FACT-C Trial Outcome Index (TOI-C), which is the sum of the CCS, physical well-being, and functional well-being subscales; and the FACT-C total score. Both cross-sectional and longitudinal analyses were used.
MIDs were stable across the different patient samples. The recommended MIDs ranged from 2 to 3 points for the CCS, 4 to 6 points for the TOI-C, and 5 to 8 points for the FACT-C total score.
MIDs can enhance the interpretability of FACT-C scores, and they can be used to provide a basis for sample size estimation and to determine clinical benefit in combination with other measures of efficacy. General guidelines for estimating MIDs for other FACT instruments are suggested.
In order to profile the lipidome for untargeted lipidomics applications, analysis by ultra-high performance liquid chromatography – high resolution mass spectrometry (UHPLC-HRMS) typically requires ...the extraction of lipid content from sample matrices using matrix-specific conditions. The Folch, Bligh-Dyer, and Matyash extraction methods, while promising approaches, were originally tailored to specific matrices (brain tissue, fish muscle, and E. coli, respectively). Each of these methods have specific solvent ratios that must be adhered to achieve optimal extraction. Thus, the sample-to-solvent ratios for these methods should be optimized for the sample matrix of interest prior to employment. This study evaluated the appropriate sample-to-extraction solvent ratios for human plasma-based lipidomics studies. An advantage of employing biphasic lipid extractions is the ability to investigate both the aqueous and organic layers for increased analyte coverage in untargeted studies. Therefore, this work also evaluated the multi-omic capability of each lipid extraction method for plasma in an effort to provide a workflow capable of increasing analyte coverage in a single extraction, thus providing a more complete understanding of complex biological systems. In plasma, a decrease in sample-to-solvent ratios from 1:4, 1:10, 1:20, to 1:100 (v/v) resulted in a gradual increase in the peak area of a diverse range of metabolite (aqueous layer) and lipid (organic layer) species for each extraction method up to the 1:20(v/v) sample-to-solvent ratio. The Bligh-Dyer and Folch methods yielded the highest peak areas at every plasma sample-to-solvent ratios for both metabolite and lipid species. Depending on the lipid class of interest, the Folch or Bligh-Dyer method is best suited for analysis of human plasma at a 1:20 (v/v) sample to total solvent ratio.
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•Evaluated sample-to-solvent ratios for plasma lipid extractions.•Evaluated the applicability of plasma multi-omic analysis for the Bligh-Dyer, Folch, and Matyash lipid extraction methods.•Plasma sample-to-solvent ratios of 1:20 (v/v) are ideal for multi-omics analysis with the Folch and Bligh-Dyer methods.•The Folch and Bligh-Dyer (aqueous layer from the 1:20 (v/v) ratio) yielded similar results to an 80% methanol extraction.
Lipids are ubiquitous and serve numerous biological functions; thus lipids have been shown to have great potential as candidates for elucidating biomarkers and pathway perturbations associated with ...disease. Methods expanding coverage of the lipidome increase the likelihood of biomarker discovery and could lead to more comprehensive understanding of disease etiology.
We introduce LipidMatch, an R-based tool for lipid identification for liquid chromatography tandem mass spectrometry workflows. LipidMatch currently has over 250,000 lipid species spanning 56 lipid types contained in in silico fragmentation libraries. Unique fragmentation libraries, compared to other open source software, include oxidized lipids, bile acids, sphingosines, and previously uncharacterized adducts, including ammoniated cardiolipins. LipidMatch uses rule-based identification. For each lipid type, the user can select which fragments must be observed for identification. Rule-based identification allows for correct annotation of lipids based on the fragments observed, unlike typical identification based solely on spectral similarity scores, where over-reporting structural details that are not conferred by fragmentation data is common. Another unique feature of LipidMatch is ranking lipid identifications for a given feature by the sum of fragment intensities. For each lipid candidate, the intensities of experimental fragments with exact mass matches to expected in silico fragments are summed. The lipid identifications with the greatest summed intensity using this ranking algorithm were comparable to other lipid identification software annotations, MS-DIAL and Greazy. For example, for features with identifications from all 3 software, 92% of LipidMatch identifications by fatty acyl constituents were corroborated by at least one other software in positive mode and 98% in negative ion mode.
LipidMatch allows users to annotate lipids across a wide range of high resolution tandem mass spectrometry experiments, including imaging experiments, direct infusion experiments, and experiments employing liquid chromatography. LipidMatch leverages the most extensive in silico fragmentation libraries of freely available software. When integrated into a larger lipidomics workflow, LipidMatch may increase the probability of finding lipid-based biomarkers and determining etiology of disease by covering a greater portion of the lipidome and using annotation which does not over-report biologically relevant structural details of identified lipid molecules.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Alphaviruses, a group of positive-sense RNA viruses, are globally distributed arboviruses capable of causing rash, arthritis, encephalitis, and death in humans. The viral replication machinery ...consists of four nonstructural proteins (nsP1–4) produced as a single polyprotein. Processing of the polyprotein occurs in a highly regulated manner, with cleavage at the P2/3 junction influencing RNA template use during genome replication. Here, we report the structure of P23 in a precleavage form. The proteins form an extensive interface and nsP3 creates a ring structure that encircles nsP2. The P2/3 cleavage site is located at the base of a narrow cleft and is not readily accessible, suggesting a highly regulated cleavage. The nsP2 protease active site is over 40 Å away from the P2/3 cleavage site, supporting a trans cleavage mechanism. nsP3 contains a previously uncharacterized protein fold with a zinc-coordination site. Known mutations in nsP2 that result in formation of noncytopathic viruses or a temperature sensitive phenotype cluster at the nsP2/nsP3 interface. Structure-based mutations in nsP3 opposite the location of the nsP2 noncytopathic mutations prevent efficient cleavage of P23, affect RNA infectivity, and alter viral RNA production levels, highlighting the importance of the nsP2/nsP3 interaction in pathogenesis. A potential RNA-binding surface, spanning both nsP2 and nsP3, is proposed based on the location of ion-binding sites and adaptive mutations. These results offer unexpected insights into viral protein processing and pathogenesis that may be applicable to other polyprotein-encoding viruses such as HIV, hepatitis C virus (HCV), and Dengue virus.
Singlet exciton fission (SF), the conversion of one spin-singlet exciton (S
) into two spin-triplet excitons (T
), could provide a means to overcome the Shockley-Queisser limit in photovoltaics. SF ...as measured by the decay of S
has been shown to occur efficiently and independently of temperature, even when the energy of S
is as much as 200 meV less than that of 2T
. Here we study films of triisopropylsilyltetracene using transient optical spectroscopy and show that the triplet pair state (TT), which has been proposed to mediate singlet fission, forms on ultrafast timescales (in 300 fs) and that its formation is mediated by the strong coupling of electronic and vibrational degrees of freedom. This is followed by a slower loss of singlet character as the excitation evolves to become only TT. We observe the TT to be thermally dissociated on 10-100 ns timescales to form free triplets. This provides a model for 'temperature-independent' efficient TT formation and thermally activated TT separation.
Evidence suggests that maintenance of vancomycin trough concentrations at between 15 and 20 mg/liter, as currently recommended, is frequently unnecessary to achieve the daily area under the ...concentration-time curve (AUC
) target of ≥400 mg · h/liter. Many patients with trough concentrations in this range have AUC
values in excess of the therapeutic threshold and within the exposure range associated with nephrotoxicity. On the basis of this, the Detroit Medical Center switched from trough concentration-guided dosing to AUC-guided dosing to minimize potentially unnecessary vancomycin exposure. The primary objective of this analysis was to assess the impact of this intervention on vancomycin-associated nephrotoxicity in a single-center, retrospective quasi-experiment of hospitalized adult patients receiving intravenous vancomycin from 2014 to 2015. The primary analysis compared the incidence of nephrotoxicity between patients monitored by assessment of the AUC
and those monitored by assessment of the trough concentration. Multivariable logistic and Cox proportional hazards regression examined the independent association between the monitoring strategy and nephrotoxicity. Secondary analysis compared vancomycin exposures (total daily dose, AUC, and trough concentrations) between monitoring strategies. Overall, 1,280 patients were included in the analysis. After adjusting for severity of illness, comorbidity, duration of vancomycin therapy, and concomitant receipt of nephrotoxins, AUC-guided dosing was independently associated with lower nephrotoxicity by both logistic regression (odds ratio, 0.52; 95% confidence interval CI, 0.34 to 0.80;
= 0.003) and Cox proportional hazards regression (hazard ratio, 0.53; 95% CI, 0.35 to 0.78;
= 0.002). AUC-guided dosing was associated with lower total daily vancomycin doses, AUC values, and trough concentrations. Vancomycin AUC-guided dosing was associated with reduced nephrotoxicity, which appeared to be a result of reduced vancomycin exposure.
The O/OREOS (Organism/Organic Exposure to Orbital Stresses) nanosatellite is the first science demonstration spacecraft and flight mission of the NASA Astrobiology Small-Payloads Program (ASP). ...O/OREOS was launched successfully on November 19, 2010, to a high-inclination (72°), 650-km Earth orbit aboard a US Air Force Minotaur IV rocket from Kodiak, Alaska. O/OREOS consists of 3 conjoined cubesat (each 1000cm3) modules: (i) a control bus; (ii) the Space Environment Survivability of Living Organisms (SESLO) experiment; and (iii) the Space Environment Viability of Organics (SEVO) experiment. Among the innovative aspects of the O/OREOS mission are a real-time analysis of the photostability of organics and biomarkers and the collection of data on the survival and metabolic activity for microorganisms at 3 times during the 6-month mission. We report on the spacecraft characteristics, payload capabilities, and present operational phase and flight data from the O/OREOS mission. The science and technology rationale of O/OREOS supports NASA′s scientific exploration program by investigating the local space environment as well as space biology relevant to Moon and Mars missions. It also serves as a precursor for experiments on small satellites, the International Space Station (ISS), future free-flyers and lunar surface exposure facilities.
► O/OREOS is the first spacecraft of NASA′s Astrobiology Small Payload Program. ► O/OREOS data answer some of astrobiology′s fundamental questions. ► O/OREOS demonstrates convincingly that cubesats can be cost-effective science platforms.
Aims. With this paper we want to investigate the highly variable afterglow light curve and environment of gamma-ray burst (GRB) 060526 at z = 3.221. Methods. We present one of the largest photometric ...datasets ever obtained for a GRB afterglow, consisting of multi-color photometric data from the ultraviolet to the near infrared. The data set contains 412 data points in total to which we add additional data from the literature. Furthermore, we present low-resolution high signal-to-noise spectra of the afterglow. The afterglow light curve is modeled with both an analytical model using broken power law fits and with a broad-band numerical model which includes energy injections. The absorption lines detected in the spectra are used to derive column densities using a multi-ion single-component curve-of-growth analysis from which we derive the metallicity of the host of GRB 060526. Results. The temporal behaviour of the afterglow follows a double broken power law with breaks at t = 0.090 ± 0.005 and t = 2.401 ± 0.061 days. It shows deviations from the smooth set of power laws that can be modeled by additional energy injections from the central engine, although some significant microvariability remains. The broadband spectral-energy distribution of the afterglow shows no significant extinction along the line of sight. The metallicity derived from S ii and Fe ii of S/H = –0.57 ± 0.25 and Fe/H = –1.09 ± 0.24 is relatively high for a galaxy at that redshift but comparable to the metallicity of other GRB hosts at similar redshifts. At the position of the afterglow, no host is detected to F775W(AB) = 28.5 mag with the HST, implying an absolute magnitude of the host M(1500 Å) > –18.3 mag which is fainter than most long-duration hosts, although the GRB may be associated with a faint galaxy at a distance of 11 kpc.
For V-shaped surface grooves in copper, we have obtained the capillary driven flow kinetics for two liquids: unreactive 1-heptanol and eutectic Sn/Pb solder, which is known to react with copper. We ...show experimentally that the flow of both liquids in these grooves follows the classical Washburn kinetics, i.e., a Poiseuille flow process, modified to include a dynamic contact angle. Because no subsidiary processes are necessary to fit our data, we propose that in this geometry capillary driven solder flow is too rapid for reaction to provide an appreciable effect. Thus, to observe the effects of Sn/Cu reaction kinetics, the flow rate must be decreased, which the present experiments allow through redesign of the groove geometry and size.
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