C5′- and C3′-sugar radicals produced via photo-excitation of one-electron oxidized adenine in 2′-deoxyadenosine and its derivatives

We report that photo-excitation of one-electron-oxidized adenine [A(-H)•] in dAdo and its 2′-deoxyribonucleotides leads to formation of deoxyribose sugar radicals in remarkably high yields. Illumination of A(-H)• in dAdo, 3′-dAMP and 5′-dAMP in aqueous glasses at 143 K leads to 80-100% conversion to sugar radicals at C5′ and C3′. The position of the phosphate in 5′- and 3′-dAMP is observed to deactivate radical formation at the site of substitution. In addition, the pH has a crucial influence on the site of sugar radical formation; e.g. at pH ∼5, photo-excitation of A(-H)• in dAdo at 143 K produces mainly C5′• whereas only C3′• is observed at high pH ∼12. (13)C substitution at C5′ in dAdo yields (13)C anisotropic couplings of (28, 28, 84) G whose isotropic component 46.7 G identifies formation of the near planar C5′•. A β-(13)C 16 G isotropic coupling from C3′• is also found. These results are found to be in accord with theoretically calculated (13)C couplings at C5′ [DFT, B3LYP, 6-31(G) level] for C5′• and C3′•. Calculations using time-dependent density functional theory [TD-DFT B3LYP, 6-31G(d)] confirm that transitions in the near UV and visible induce hole transfer from the base radical to the sugar group leading to sugar radical formation

The Arecibo Galaxy Environment Survey XII : Optically dark HI clouds in the Leo I Group

Using data from the Arecibo Galaxy Environment Survey, we report the discovery of five HI clouds in the Leo I group without detected optical counterparts. Three of the clouds are found midway between M96 and M95, one is only 10$^{\prime}$ from the south-east side of the well-known Leo Ring, and the fifth is relatively isolated. HI masses range from 2.6$\times$10$^{6}$ - 9.0$\times$10$^{6}$M$_{\odot}$ and velocity widths (W50) from 16 - 42 km/s. Although a tidal origin is the most obvious explanation, this formation mechanism faces several challenges. For the most isolated cloud, the difficulties are its distance from neighbouring galaxies and the lack of any signs of disturbance in the HI discs of those systems. Some of the clouds also appear to follow the baryonic Tully-Fisher relation between mass and velocity width for normal, stable galaxies which is not expected if they are tidal in origin. Three clouds are found between M96 and M95 which have no optical counterparts, but have otherwise similar properties and location to the optically detected galaxy LeG 13. While overall we favour a tidal debris scenario to explain the clouds, we cannot rule out a primordial origin. If the clouds were produced in the same event that gave rise to the Leo Ring, they may provide important constraints on any model attempting to explain that structureComment: 16 pages (plus 4 page appendix), 1 table, 7 figures, accepted for publication in A

Development of a novel non-invasive biomarker panel for hepatic fibrosis in MASLD

Accurate non-invasive biomarkers to diagnose metabolic dysfunction-associated steatotic liver disease (MASLD)-related fibrosis are urgently needed. This study applies a translational approach to develop a blood-based biomarker panel for fibrosis detection in MASLD. A molecular gene expression signature identified from a diet-induced MASLD mouse model (LDLr−/−.Leiden) is translated into human blood-based biomarkers based on liver biopsy transcriptomic profiles and protein levels in MASLD patient serum samples. The resulting biomarker panel consists of IGFBP7, SSc5D and Sema4D. LightGBM modeling using this panel demonstrates high accuracy in predicting MASLD fibrosis stage (F0/F1: AUC = 0.82; F2: AUC = 0.89; F3/F4: AUC = 0.87), which is replicated in an independent validation cohort. The overall accuracy of the model outperforms predictions by the existing markers Fib-4, APRI and FibroScan. In conclusion, here we show a disease mechanism-related blood-based biomarker panel with three biomarkers which is able to identify MASLD patients with mild or advanced hepatic fibrosis with high accuracy.</p

Development of a novel non-invasive biomarker panel for hepatic fibrosis in MASLD

Accurate non-invasive biomarkers to diagnose metabolic dysfunction-associated steatotic liver disease (MASLD)-related fibrosis are urgently needed. This study applies a translational approach to develop a blood-based biomarker panel for fibrosis detection in MASLD. A molecular gene expression signature identified from a diet-induced MASLD mouse model (LDLr−/−.Leiden) is translated into human blood-based biomarkers based on liver biopsy transcriptomic profiles and protein levels in MASLD patient serum samples. The resulting biomarker panel consists of IGFBP7, SSc5D and Sema4D. LightGBM modeling using this panel demonstrates high accuracy in predicting MASLD fibrosis stage (F0/F1: AUC = 0.82; F2: AUC = 0.89; F3/F4: AUC = 0.87), which is replicated in an independent validation cohort. The overall accuracy of the model outperforms predictions by the existing markers Fib-4, APRI and FibroScan. In conclusion, here we show a disease mechanism-related blood-based biomarker panel with three biomarkers which is able to identify MASLD patients with mild or advanced hepatic fibrosis with high accuracy.</p

The EFF-1A Cytoplasmic Domain Influences Hypodermal Cell Fusions in C. elegans But Is Not Dependent on 14-3-3 Proteins.

BACKGROUND: Regulatory and biophysical mechanisms of cell-cell fusion are largely unknown despite the fundamental requirement for fused cells in eukaryotic development. Only two cellular fusogens that are not of clear recent viral origin have been identified to date, both in nematodes. One of these, EFF-1, is necessary for most cell fusions in Caenorhabditis elegans. Unregulated EFF-1 expression causes lethality due to ectopic fusion between cells not developmentally programmed to fuse, highlighting the necessity of tight fusogen regulation for proper development. Identifying factors that regulate EFF-1 and its paralog AFF-1 could lead to discovery of molecular mechanisms that control cell fusion upstream of the action of a membrane fusogen. Bioinformatic analysis of the EFF-1A isoform\u27s predicted cytoplasmic domain (endodomain) previously revealed two motifs that have high probabilities of interacting with 14-3-3 proteins when phosphorylated. Mutation of predicted phosphorylation sites within these motifs caused measurable loss of eff-1 gene function in cell fusion in vivo. Moreover, a human 14-3-3 isoform bound to EFF-1::GFP in vitro. We hypothesized that the two 14-3-3 proteins in C. elegans, PAR-5 and FTT-2, may regulate either localization or fusion-inducing activity of EFF-1. METHODOLOGY/PRINCIPAL FINDINGS: Timing of fusion events was slightly but significantly delayed in animals unable to produce full-length EFF-1A. Yet, mutagenesis and live imaging showed that phosphoserines in putative 14-3-3 binding sites are not essential for EFF-1::GFP accumulation at the membrane contact between fusion partner cells. Moreover, although the EFF-1A endodomain was required for normal rates of eff-1-dependent epidermal cell fusions, reduced levels of FTT-2 and PAR-5 did not visibly affect the function of wild-type EFF-1 in the hypodermis. CONCLUSIONS/SIGNIFICANCE: Deletion of the EFF-1A endodomain noticeably affects the timing of hypodermal cell fusions in vivo. However, prohibiting phosphorylation of candidate 14-3-3-binding sites does not impact localization of the fusogen. Hypodermal membrane fusion activity persists when 14-3-3 expression levels are reduced

Effect of Hydrocortisone on Mortality and Organ Support in Patients With Severe COVID-19: The REMAP-CAP COVID-19 Corticosteroid Domain Randomized Clinical Trial.

Importance: Evidence regarding corticosteroid use for severe coronavirus disease 2019 (COVID-19) is limited. Objective: To determine whether hydrocortisone improves outcome for patients with severe COVID-19. Design, Setting, and Participants: An ongoing adaptive platform trial testing multiple interventions within multiple therapeutic domains, for example, antiviral agents, corticosteroids, or immunoglobulin. Between March 9 and June 17, 2020, 614 adult patients with suspected or confirmed COVID-19 were enrolled and randomized within at least 1 domain following admission to an intensive care unit (ICU) for respiratory or cardiovascular organ support at 121 sites in 8 countries. Of these, 403 were randomized to open-label interventions within the corticosteroid domain. The domain was halted after results from another trial were released. Follow-up ended August 12, 2020. Interventions: The corticosteroid domain randomized participants to a fixed 7-day course of intravenous hydrocortisone (50 mg or 100 mg every 6 hours) (n = 143), a shock-dependent course (50 mg every 6 hours when shock was clinically evident) (n = 152), or no hydrocortisone (n = 108). Main Outcomes and Measures: The primary end point was organ support-free days (days alive and free of ICU-based respiratory or cardiovascular support) within 21 days, where patients who died were assigned -1 day. The primary analysis was a bayesian cumulative logistic model that included all patients enrolled with severe COVID-19, adjusting for age, sex, site, region, time, assignment to interventions within other domains, and domain and intervention eligibility. Superiority was defined as the posterior probability of an odds ratio greater than 1 (threshold for trial conclusion of superiority >99%). Results: After excluding 19 participants who withdrew consent, there were 384 patients (mean age, 60 years; 29% female) randomized to the fixed-dose (n = 137), shock-dependent (n = 146), and no (n = 101) hydrocortisone groups; 379 (99%) completed the study and were included in the analysis. The mean age for the 3 groups ranged between 59.5 and 60.4 years; most patients were male (range, 70.6%-71.5%); mean body mass index ranged between 29.7 and 30.9; and patients receiving mechanical ventilation ranged between 50.0% and 63.5%. For the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively, the median organ support-free days were 0 (IQR, -1 to 15), 0 (IQR, -1 to 13), and 0 (-1 to 11) days (composed of 30%, 26%, and 33% mortality rates and 11.5, 9.5, and 6 median organ support-free days among survivors). The median adjusted odds ratio and bayesian probability of superiority were 1.43 (95% credible interval, 0.91-2.27) and 93% for fixed-dose hydrocortisone, respectively, and were 1.22 (95% credible interval, 0.76-1.94) and 80% for shock-dependent hydrocortisone compared with no hydrocortisone. Serious adverse events were reported in 4 (3%), 5 (3%), and 1 (1%) patients in the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively. Conclusions and Relevance: Among patients with severe COVID-19, treatment with a 7-day fixed-dose course of hydrocortisone or shock-dependent dosing of hydrocortisone, compared with no hydrocortisone, resulted in 93% and 80% probabilities of superiority with regard to the odds of improvement in organ support-free days within 21 days. However, the trial was stopped early and no treatment strategy met prespecified criteria for statistical superiority, precluding definitive conclusions. Trial Registration: ClinicalTrials.gov Identifier: NCT02735707

The UV-vis absorption spectrum of A(-H)• produced by Cl• oxidation of dAdo, at 77 K in 7 M LiCl glass/DO

<p><b>Copyright information:</b></p><p>Taken from "C5′- and C3′-sugar radicals produced via photo-excitation of one-electron oxidized adenine in 2′-deoxyadenosine and its derivatives"</p><p>Nucleic Acids Research 2006;34(5):1501-1511.</p><p>Published online 14 Mar 2006</p><p>PMCID:PMC1401510.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> This absorption imparts a purple color to the sample

Schematic representation of the mechanism of sugar radical formation in dAdo using C5′• formation as an example

<p><b>Copyright information:</b></p><p>Taken from "C5′- and C3′-sugar radicals produced via photo-excitation of one-electron oxidized adenine in 2′-deoxyadenosine and its derivatives"</p><p>Nucleic Acids Research 2006;34(5):1501-1511.</p><p>Published online 14 Mar 2006</p><p>PMCID:PMC1401510.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p

Spectra obtained for identically prepared samples of dAdo (A–D) and 5′-CdAdo (E–H) in 7 M LiCl glasses

<p><b>Copyright information:</b></p><p>Taken from "C5′- and C3′-sugar radicals produced via photo-excitation of one-electron oxidized adenine in 2′-deoxyadenosine and its derivatives"</p><p>Nucleic Acids Research 2006;34(5):1501-1511.</p><p>Published online 14 Mar 2006</p><p>PMCID:PMC1401510.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> () ESR spectrum found after oxidation of dAdo by Cl• consisting of A(-H)•(50%) (the central singlet, ) and C3′• (25%) (). () After illumination of the sample in A with visible light for 60 min at 143 K, the A(-H)• signal is lost by ∼80% and the C3′• signal is increased. () Spectrum assigned to C3′• obtained by subtraction of the A(-H)• signal (20%) from spectrum (B). () Simulation of the spectrum in (C) for C3′• using the parameters given in the text. () ESR spectrum recorded after oxidation of [5′-C]dAdo by Cl• consisting of A(-H)• and C3′•. () After illumination of the sample in E for 40 min at 143 K. () C3′• spectrum showing a 16 G β-C coupling found by subtraction of the A(-H)• signal from spectrum (F). () Simulation of the spectrum in G using parameters given in the text. All spectra were recorded at 77 K

() ESR spectrum of A(-H)• formed by oxidation of dAdo in 7 M LiCl glass/DO with Cl•

<p><b>Copyright information:</b></p><p>Taken from "C5′- and C3′-sugar radicals produced via photo-excitation of one-electron oxidized adenine in 2′-deoxyadenosine and its derivatives"</p><p>Nucleic Acids Research 2006;34(5):1501-1511.</p><p>Published online 14 Mar 2006</p><p>PMCID:PMC1401510.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> () Spectrum after illumination with visible light for 45 min at 143 K, containing contributions from 80% C5′•, 15% C3′• and 5% C1′•. () Spectrum found after subtraction of C1′• and C3′• components () from spectrum (B). This doublet is attributed to C5′•. () ESR spectrum from A(-H)• in [5′-C]dAdo in 7 M LiCl glass/DO. () Spectrum after illumination for 70 min with visible light at 143 K. This spectrum is made up of 80% C5′• and 20% C3′•; both radicals possess substantial C couplings ( and ). () Spectrum obtained after subtraction of simulated C3′• spectrum (20%) () and of A(-H)• spectrum (15%) () from (D). This spectrum is assigned to C5′• (see text). () Simulation of spectrum in (F) using the parameters given in the text and in and . All spectra were recorded at 77 K