Mechanistic Studies of Small Molecule Ligands Selective to RNA Single G Bulges.

Small-molecule RNA binders have emerged as an important pharmacological modality. A profound understanding of the ligand selectivity, binding mode, and influential factors governing ligand engagement with RNA targets is the foundation for rational ligand design. Here, we report a novel class of coumarin derivatives exhibiting selective binding affinity towards single G RNA bulges.

Nanosecond chain dynamics of single-stranded nucleic acids.

The conformational dynamics of single-stranded nucleic acids are fundamental for nucleic acid folding and function. However, their elementary chain dynamics have been difficult to resolve experimentally. Here we employ a combination of single-molecule Förster resonance energy transfer, nanosecond fluorescence correlation spectroscopy, and nanophotonic enhancement to determine the conformational ensembles and rapid chain dynamics of short single-stranded nucleic acids in solution.

Donor plasma VEGF-A as a biomarker for myocardial injury and primary graft dysfunction after heart transplantation.

Background: Vascular endothelial growth factor (VEGF)-A is an angiogenic and proinflammatory cytokine with profound effects on microvascular permeability and vasodilation. Several processes may induce VEGF-A expression in brain-dead organ donors. However, it remains unclear whether donor VEGF-A is linked to adverse outcomes after heart transplantation.

Conformational dynamics of the hepatitis C virus 3'X RNA.

The 3' end of the hepatitis C virus genome is terminated by a highly conserved, 98 nt sequence called 3'X. This untranslated structural element is thought to regulate several essential RNA-dependent processes associated with infection. 3'X has two proposed conformations comprised of either three or two stem-loop structures that result from the different base-pairing interactions within the first 55 nt.

Large-scale analysis of interobserver agreement and reliability in cardiotocography interpretation during labor using an online tool.

Background: While the effectiveness of cardiotocography in reducing neonatal morbidity is still debated, it remains the primary method for assessing fetal well-being during labor. Evaluating how accurately professionals interpret cardiotocography signals is essential for its effective use. The objective was to evaluate the accuracy of fetal hypoxia prediction by practitioners through the interpretation of cardiotocography signals and clinical variables during labor.

Current and future drought vulnerability for three dominant boreal tree species.

Climate change is projected to increase the frequency and severity of droughts, possibly causing sudden and elevated tree mortality. Better understanding and predictions of boreal forest responses to climate change are needed to efficiently adapt forest management. We used tree-ring width chronologies from the Swedish National Forest Inventory, sampled between 2010 and 2018, and a random forest machine-learning algorithm to identify the tree, stand, and site variables that determine drought damage risk, and to predict their future spatial-temporal evolution.

Mechanism of Ligand Binding to Theophylline RNA Aptamer.

Studying RNA-ligand interactions and quantifying their binding thermodynamics and kinetics are of particular relevance in the field of drug discovery. Here, we combined biochemical binding assays and accelerated molecular simulations to investigate ligand binding and dissociation in RNA using the theophylline-binding RNA as a model system. All-atom simulations using a Ligand Gaussian accelerated Molecular Dynamics method (LiGaMD) have captured repetitive binding and dissociation of theophylline and caffeine to RNA.

Potential implications of shortened rotation length for forest birds, bryophytes, lichens and vascular plants: An example from southern Swedish production forests.

The rotation lengths of intensively managed production forests may be altered to achieve a variety of goals, with correspondingly implications for biodiversity. Here we consider the potential implications of shortened rotation times for biodiversity in planted monocultures of the two most common production tree species in Sweden, Scots pine (Pinus sylvestris) and Norway spruce (Picea abies). To do so we surveyed bird, bryophyte, epiphytic lichen and vascular plant diversity in 80 and 55-year-old stands; stand ages which approximate present-day and potential future rotation lengths in this region respectively.

Transcriptomic Landscape of Circulating Extracellular Vesicles in Heart Transplant Ischemia-Reperfusion.

Ischemia-reperfusion injury (IRI) is an inevitable event during heart transplantation, which is known to exacerbate damage to the allograft. However, the precise mechanisms underlying IRI remain incompletely understood. Here, we profiled the whole transcriptome of plasma extracellular vesicles (EVs) by RNA sequencing from 41 heart transplant recipients immediately before and at 12 h after transplant reperfusion.

Single-molecule-binding studies of antivirals targeting the hepatitis C virus core protein.

The hepatitis C virus is associated with nearly 300,000 deaths annually. At the core of the virus is an RNA-protein complex called the nucleocapsid, which consists of the viral genome and many copies of the core protein. Because the assembly of the nucleocapsid is a critical step in viral replication, a considerable amount of effort has been devoted to identifying antiviral therapeutics that can bind to the core protein and disrupt assembly.

DeepCTG® 1.0: an interpretable model to detect fetal hypoxia from cardiotocography data during labor and delivery.

Introduction: Cardiotocography, which consists in monitoring the fetal heart rate as well as uterine activity, is widely used in clinical practice to assess fetal wellbeing during labor and delivery in order to detect fetal hypoxia and intervene before permanent damage to the fetus. We present DeepCTG® 1.0, a model able to predict fetal acidosis from the cardiotocography signals.

Severe primary graft dysfunction of the heart transplant is associated with increased plasma and intragraft proinflammatory cytokine expression.

Introduction: Heart transplant results have constantly improved but primary left ventricle graft dysfunction (LV-PGD) remains a devastating complication early after transplantation. Donor and recipient systemic inflammatory response may be involved in immune activation of the transplant, and LV-PGD development. Here, we investigated donor and recipient plasma and intragraft cytokine profiles preoperatively and during LV-PGD and searched for predictive markers for LV-PGD.

Apolar chemical environments compact unfolded RNAs and can promote folding.

It is well documented that the structure, and thus function, of nucleic acids depends on the chemical environment surrounding them, which often includes potential proteinaceous binding partners. The nonpolar amino acid side chains of these proteins will invariably alter the polarity of the local chemical environment around the nucleic acid. However, we are only beginning to understand how environmental polarity generally influences the structural and energetic properties of RNA folding.

Plasma proteome of brain-dead organ donors predicts heart transplant outcome.

Background: The pathophysiological changes related to brain death may affect the quality of the transplanted organs and expose the recipients to risks. We probed systemic changes reflected in donor plasma proteome and investigated their relationship to heart transplant outcomes.

Methods: Plasma samples from brain-dead multi-organ donors were analyzed by label-free protein quantification using high-definition mass spectrometry.

Intensive care-treated cardiac arrest: a retrospective study on the impact of extended age on mortality, neurological outcome, received treatments and healthcare-associated costs.

Background: Cardiac arrest (CA) is a leading cause of death worldwide. As population ages, the need for research focusing on CA in elderly increases. This study investigated treatment intensity, 12-month neurological outcome, mortality and healthcare-associated costs for patients aged over 75 years treated for CA in an intensive care unit (ICU) of a tertiary hospital.

Recognition of single-stranded nucleic acids by small-molecule splicing modulators.

Risdiplam is the first approved small-molecule splicing modulator for the treatment of spinal muscular atrophy (SMA). Previous studies demonstrated that risdiplam analogues have two separate binding sites in exon 7 of the SMN2 pre-mRNA: (i) the 5'-splice site and (ii) an upstream purine (GA)-rich binding site. Importantly, the sequence of this GA-rich binding site significantly enhanced the potency of risdiplam analogues.

Microwave scan and brain biomarkers to rule out intracranial hemorrhage: study protocol of a planned prospective study (MBI01).

Purpose: The aim of this planned study is to evaluate the ability of a cranial microwave scanner in conjunction with nine brain biomarkers (Aβ40, Aβ42, GFAP, H-FABP, S100B, NF-L, NSE, UCH-L1 and IL-10) to detect and rule out traumatic intracranial hemorrhage in an emergency department setting. Traumatic brain injury is a world-wide topic of interest for researchers and clinicians. It affects 2% of the population per annum and presents challenges for physicians as patients' initial signs and symptoms do not always correlate with the extent of brain injury.

The SARS-CoV-2 Conserved Macrodomain Is a Mono-ADP-Ribosylhydrolase.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other SARS-related CoVs encode 3 tandem macrodomains within nonstructural protein 3 (nsp3). The first macrodomain, Mac1, is conserved throughout CoVs and binds to and hydrolyzes mono-ADP-ribose (MAR) from target proteins. Mac1 likely counters host-mediated antiviral ADP-ribosylation, a posttranslational modification that is part of the host response to viral infections.

Real-time compaction of nanoconfined DNA by an intrinsically disordered macromolecular counterion.

We demonstrate how a recently developed nanofluidic device can be used to study protein-induced compaction of genome-length DNA freely suspended in solution. The protein we use in this study is the hepatitis C virus core protein (HCVcp), which is a positively charged, intrinsically disordered protein. Using nanofluidic devices in combination with fluorescence microscopy, we observe that protein-induced compaction preferentially begins at the ends of linear DNA.

The SARS-CoV-2 conserved macrodomain is a mono-ADP-ribosylhydrolase.

Unlabelled: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other SARS-like-CoVs encode 3 tandem macrodomains within non-structural protein 3 (nsp3). The first macrodomain, Mac1, is conserved throughout CoVs, and binds to and hydrolyzes mono-ADP-ribose (MAR) from target proteins. Mac1 likely counters host-mediated anti-viral ADP-ribosylation, a posttranslational modification that is part of the host response to viral infections.