Weak-cooperative binding of a long single-stranded DNA chain on a surface.

Binding gene-wide single-stranded nucleic acids to surface-immobilized complementary probes is an important but challenging process for biophysical studies and diagnostic applications. The challenge comes from the conformational dynamics of the long chain that affects its accessibility and weakens its hybridization to the probes. We investigated the binding of bacteriophage genome M13mp18 on several different 20-mer probes immobilized on the surface of a multi-spot, label-free biosensor, and observed that only a few of them display strong binding capability with dissociation constant as low as 10 pM. Comparing experimental data and computational analysis of the M13mp18 chain structural features, we found that the capturing performance of a specific probe is directly related to the multiplicity of binding sites on the genomic strand, and poorly connected with the predicted secondary and tertiary structure. We show that a model of weak cooperativity of transient bonds is compatible with the measured binding kinetics and accounts for the enhancement of probe capturing observed when more than 20 partial pairings with binding free energy lower than -10 kcal mol-1 are present. This mechanism provides a specific pattern of response of a genomic strand on a panel of properly selected oligomer probe sequences.

Explosive electrostatic instability of ferroelectric liquid droplets on ferroelectric solid surfaces.

We investigated the electrostatic behavior of ferroelectric liquid droplets exposed to the pyroelectric field of a lithium niobate ferroelectric crystal substrate. The ferroelectric liquid is a nematic liquid crystal, in which almost complete polar ordering of the molecular dipoles generates an internal macroscopic polarization locally collinear to the mean molecular long axis. Upon entering the ferroelectric phase by reducing the temperature from the nematic phase, the liquid crystal droplets become electromechanically unstable and disintegrate by the explosive emission of fluid jets. These jets are mostly interfacial, spreading out on the substrate surface, and exhibit fractal branching out into smaller streams to eventually disrupt, forming secondary droplets. We understand this behavior as a manifestation of the Rayleigh instability of electrically charged fluid droplets, expected when the electrostatic repulsion exceeds the surface tension of the fluid. In this case, the charges are due to the bulk polarization of the ferroelectric fluid, which couples to the pyroelectric polarization of the underlying lithium niobate substrate through its fringing field and solid-fluid interface coupling. Since the ejection of fluid does not neutralize the droplet surfaces, they can undergo multiple explosive events as the temperature decreases.

Simulating the Lyotropic Phase Behavior of a Partially Self-Complementary DNA Tetramer.

DNA oligomers in solution have been found to develop liquid crystal phases via a hierarchical process that involves Watson-Crick base pairing, supramolecular assembly into columns of duplexes, and long-range ordering. The multiscale nature of this phenomenon makes it difficult to quantitatively describe and assess the importance of the various contributions, particularly for very short strands. We performed molecular dynamics simulations based on the coarse-grained oxDNA model, aiming to depict all of the assembly processes involved and the phase behavior of solutions of the DNA GCCG tetramers. We find good quantitative matching to experimental data at both levels of molecular association (thermal melting) and collective ordering (phase diagram). We characterize the isotropic state and the low-density nematic and high-density columnar liquid crystal phases in terms of molecular order, size of aggregates, and structure, together with their effects on diffusivity processes. We observe a cooperative aggregation mechanism in which the formation of dimers is less thermodynamically favored than the formation of longer aggregates.

Fluid jets and polar domains, on the relationship between electromechanical instability and topology in ferroelectric nematic liquid crystal droplets.

Ferroelectric nematic liquid crystals are a class of recently discovered fluid materials formed by highly polar molecules that spontaneously align along a common direction, giving rise to a macroscopic polarization P. Since the polarization vector is locally collinear to the optical axis n, the study of the spatial patterns of n enables deducing the structure of P. We have carried on such topological study on ferroelectric nematic droplets confined between two solid ferroelectric substrates both when the droplet is in equilibrium and during a jet-emission phase that takes place when the solid surfaces become sufficiently charged. We find that in equilibrium the droplet splits in striped domains in which P has alternating directions. When these domains extend close to the droplets' perimeter, P adopts a π-twisted structure to minimize accumulation of polarization charges. As the substrate surface charge is increased above threshold, fluid jets are emitted with a quasi-periodic pattern, a behaviour suggesting that their location is governed by an electrofluidic instability on the droplets' rim, in turn indicating the absence of specific trigger points. Soon after their emission, the jet periodicity is lost; some jets retract while other markedly grow. In this second regime, jets that grow are those that more easily connect to polar domains with P along the jet axis. Occasionally, ejection of isolated spikes also occurs, revealing locations where polarization charges have accumulated because of topological patterns extending on length scales smaller than the typical domain size.

Difficult Intravascular Access in Pediatric Emergency Department: The Ultrasound-Assisted Strategy (DIAPEDUS Study).

Vein line positioning represents one of the first diagnostic and therapeutic steps in Pediatric Emergency Department (PED); however, the outcome of this maneuver is frequently not as expected, especially for difficult-to-access (DIVA) patients. The standard technique (visual-palpatory) has a low success rate; hence ultrasound (US) assistance has been suggested for DIVA patients, although controversial results have been obtained. Our study compared the success rate of an intravascular (IV) access procedure at the first attempt, with and without ultrasound assistance, in pediatric DIVA patients. Secondary objectives were the global success rate, the mean procedural time, the IV device's life span, and the complications rate. We conducted an observational, prospective, monocentric, no-profit cohort study enrolling 110 patients presenting to our ED, aged 0-21 years. All the patients were considered difficult-to-access patients according to the DIVA score (≥4) or history of previous difficult intravascular access. They were randomized into two homogeneous groups: 50 patients with the standard and 60 with the US-assisted technique. We obtained a significantly higher success rate at first attempt with the US-guided technique (90% vs 18%, p ≤ .00001). Moreover, the overall success rate was higher in the US group (95% vs 46%, p < .00001). The mean procedural time resulted significantly less in the US group (2.7 ± 2.2 min vs 10 ± 6.4 min, p < .0001), as well as the overall number of attempts to obtain a stable IV line (1.09 ± 0.34 attempts vs 2.38 ± 1.09 attempts, p < .0001). We experienced some post-procedural complications without differences in the two groups, although none were severe. Our study showed that bedside ultrasound assisting implantation of peripheral venous access in pediatric DIVA patients improves first-time success rate, overall success rate, procedural time, and patient comfort, reducing the number of attempts to obtain a stable IV line.

Clinical course and peculiarities of Parechovirus and Enterovirus central nervous system infections in newborns: a single-center experience.

Parechovirus (HpEV) and Enterovirus (EV) infections in children mostly have a mild course but are particularly fearsome in newborns in whom they may cause aseptic meningitis, encephalitis, and myocarditis. Our study aimed to describe the clinical presentations and peculiarities of CNS infection by HpEV and EV in neonates. This is a single-center retrospective study at Istituto Gaslini, Genoa, Italy. Infants aged ≤ 30 days with a CSF RTq-PCR positive for EV or HpEV from January 1, 2022, to December 1, 2023, were enrolled. Each patient's record included demographic data, blood and CSF tests, brain MRI, therapies, length of stay, ICU admission, complications, and mortality. The two groups were compared to identify any differences and similarities. Twenty-five patients (15 EV and 10 HpEV) with a median age of 15 days were included. EV patients had a more frequent history of prematurity/neonatal respiratory distress syndrome (p = 0.021), more respiratory symptoms on admission (p = 0.012), and higher C-reactive protein (CRP) levels (p = 0.027), whereas ferritin values were significantly increased in HpEV patients (p = 0.001). Eight patients had a pathological brain MRI, equally distributed between the two groups. Three EV patients developed myocarditis and one HpEV necrotizing enterocolitis with HLH-like. No deaths occurred.  Conclusion: EV and HpEV CNS infections are not easily distinguishable by clinical features. In both cases, brain MRI abnormalities are not uncommon, and a severe course of the disease is possible. Hyper-ferritinemia may represent an additional diagnostic clue for HpEV infection, and its monitoring is recommended to intercept HLH early and initiate immunomodulatory treatment. Larger studies are needed to confirm our findings. What is Known: • Parechovirus and Enteroviruses are the most common viral pathogens responsible for sepsis and meningoencephalitis in neonates and young infants. • The clinical course and distinguishing features of Parechovirus and Enterovirus central nervous system infections are not well described. What is New: • Severe disease course, brain MRI abnormalities, and complications are not uncommon in newborns with Parechovirus and Enteroviruses central nervous system infections. • Hyper-ferritinemia may represent an additional diagnostic clue for Parechovirus infection and its monitoring is recommended.

In silico study of DNA mononucleotide self-assembly.

Recent experiments have demonstrated the self-assembly and long-range ordering of concentrated aqueous solutions of DNA and RNA mononucleotides. These are found to form Watson-Crick pairs that stack into columns that become spatially organized into a columnar liquid-crystalline phase. In this work, we numerically investigate this phase behavior by adopting an extremely coarse-grained model in which nucleotides are represented as semi-disk-like polyhedra decorated with attractive (patchy) sites that mimic the stacking and pairing interactions. We carry out Monte Carlo simulations of these patchy polyhedra by adapting algorithms borrowed from computer graphics. This model reproduces the features of the experimental phase behavior, which essentially depends on the combination of pairing and stacking interactions.

Ten new paediatric emergency medicine commandments.

AIM: We suggest the top ten tips that any clinician working in a pediatric emergency department should always keep in mind. METHODS: A literature review was conducted using, as a starting point, the previously published Ten Commandments for Emergency Medicine, Pediatric Emergency Medicine, and Perinatal Medicine. RESULTS AND CONCLUSION: A standard curriculum for pediatric emergency physicians is lacking. These ten commandments should be considered as advice for physicians who practice this profession every day and not as unbreakable rules established from above.

Epidemiological and clinical evolution of multisystem inflammatory syndrome in children throughout the SARS-CoV-2 pandemic in a tertiary Italian children's hospital.

Multisystem inflammatory syndrome in children (MIS-C) is a potentially life-threatening disease temporally linked to SARS-CoV-2 whose incidence and clinical presentation may have been altered by the different SARS-CoV-2 variants and by vaccination. METHODS: We retrospectively collected the data of all MIS-C cases admitted to the Gaslini Children's Hospital, the hub for SARS-CoV-2 related diseases in Liguria region, Italy, from 01 October 2020, to 30 November 2022, evaluating the ratio between MIS-C cases and (1) COVID-19 paediatric cases in our region, (2) emergency department admissions and (3) emergency department febrile patients. We also compared MIS-C incidence in pre- post-vaccination periods. RESULTS: We observed a significant global decline in the incidence of MIS-Cover the four variant periods and after the starting of vaccination whereas clinical features, therapeutic management and severity did not significantly vary. CONCLUSIONS: In our setting, we demonstrated a significant decrease of MIS-C incidence according to the predominant variant and including not vaccinated children. Regardless of variant type, the patients showed similar phenotypes and severity throughout the pandemic. SARS-CoV-2 variants as well as immune protection after previous infections and/or vaccination may have interacted by playing different roles and reducing the incidence of MIS-C.

Digital Detection of Single Virus Particles by Multi-Spot, Label-Free Imaging Biosensor on Anti-Reflective Glass.

Rapid detection of whole virus particles in biological or environmental samples represents an unmet need for the containment of infectious diseases. Here, an optical device enabling the enumeration of single virion particles binding on antibody or aptamers immobilized on a surface with anti-reflective coating is described. In this regime, nanoparticles adhering to the sensor surface provide localized contributions to the reflected field that become detectable because of their mixing with the interfering waves in the reflection direction. Thus, these settings are exploited to realize a scan-free, label-free, micro-array-type digital assay on a disposable cartridge, in which the virion counting takes place in wide field-of-view imaging. With this approach we could quantify, by enumeration, different variants of SARS-CoV-2 virions interacting with antibodies and aptamers immobilized on different spots. For all tested variants, the aptamers showed larger affinity but lower specificity relative to the antibodies. It is found that the combination of different probes on the same surface enables increasing specificity of detection and dynamic range.

Pairing statistics and melting of random DNA oligomers: Finding your partner in superdiverse environments.

Understanding of the pairing statistics in solutions populated by a large number of distinct solute species with mutual interactions is a challenging topic, relevant in modeling the complexity of real biological systems. Here we describe, both experimentally and theoretically, the formation of duplexes in a solution of random-sequence DNA (rsDNA) oligomers of length L = 8, 12, 20 nucleotides. rsDNA solutions are formed by 4L distinct molecular species, leading to a variety of pairing motifs that depend on sequence complementarity and range from strongly bound, fully paired defectless helices to weakly interacting mismatched duplexes. Experiments and theory coherently combine revealing a hybridization statistics characterized by a prevalence of partially defected duplexes, with a distribution of type and number of pairing errors that depends on temperature. We find that despite the enormous multitude of inter-strand interactions, defectless duplexes are formed, involving a fraction up to 15% of the rsDNA chains at the lowest temperatures. Experiments and theory are limited here to equilibrium conditions.

Supratentorial Demyelinating Lesions Following Severe Acute Respiratory Syndrome Coronavirus-2 Infection: A Pediatric Case Report.

INTRODUCTION: Most coronavirus disease 2019 (COVID-19) pediatric patients are asymptomatic; however, several neurological manifestations associated with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection have been reported. Demyelinating events such as acute disseminated encephalomyelitis have been recently included among potential complications of COVID-19. CASE REPORT: We describe the case of a 12-year-old boy who developed central nervous system demyelinating lesions following SARS-CoV-2 infection. Two months prior he had been diagnosed with panuveitis but was otherwise healthy. Three weeks after testing positive for SARS-CoV-2, he started to complain of right temporal headache associated with right orbital pain without vision impairment. Brain magnetic resonance imaging showed large leukodystrophy-like demyelinating lesions. Standard electroencephalogram revealed a slow activity on the right hemisphere. His clinical and electroencephalographic course was favorable, with a good response to corticosteroid therapy and infusions of intravenous immunoglobulins. Delayed but complete resolution of brain lesions was noted on imaging. CONCLUSION: Our case contributes to broaden the knowledge regarding the spectrum of possible complications of SARS-CoV-2 infection. The relative lack of clinical manifestations in our patient can be seen as a warning not to underestimate even mild neurological symptoms correlated with COVID-19.

VID22 counteracts G-quadruplex-induced genome instability.

Genome instability is a condition characterized by the accumulation of genetic alterations and is a hallmark of cancer cells. To uncover new genes and cellular pathways affecting endogenous DNA damage and genome integrity, we exploited a Synthetic Genetic Array (SGA)-based screen in yeast. Among the positive genes, we identified VID22, reported to be involved in DNA double-strand break repair. vid22Δ cells exhibit increased levels of endogenous DNA damage, chronic DNA damage response activation and accumulate DNA aberrations in sequences displaying high probabilities of forming G-quadruplexes (G4-DNA). If not resolved, these DNA secondary structures can block the progression of both DNA and RNA polymerases and correlate with chromosome fragile sites. Vid22 binds to and protects DNA at G4-containing regions both in vitro and in vivo. Loss of VID22 causes an increase in gross chromosomal rearrangement (GCR) events dependent on G-quadruplex forming sequences. Moreover, the absence of Vid22 causes defects in the correct maintenance of G4-DNA rich elements, such as telomeres and mtDNA, and hypersensitivity to the G4-stabilizing ligand TMPyP4. We thus propose that Vid22 is directly involved in genome integrity maintenance as a novel regulator of G4 metabolism.

Individual, environmental and demographic factors may play a role in the prognosis of fatal and non-fatal paediatric drowning.

AIM: Drowning is a leading cause of unintentional death. Ongoing efforts are dedicated to preventing these tragic incidents. Our aim was to evaluate whether demographic, environmental and epidemiological characteristics of drowned children influence their prognosis. METHODS: Single-centre retrospective study spanning 12 years. Each patient's record included: age, sex, place of residence, presence of siblings, season of incident, location of event, associated trauma, loss of consciousness, need for cardiopulmonary resuscitation, intubation, admission to intensive care unit, length of stay and mortality. RESULTS: We enrolled 60 patients, with a mean age of 5.9 ± 3.4 years; 63.5% were male. Children who did not reside near the sea were significantly older than those who did (p = 0.01) and faced a higher risk of experiencing sea-related drowning (p = 0.05). No patients died. Loss of consciousness and need for cardiopulmonary resuscitation were recorded in 30 and 19 patients respectively. Seven patients sustained trauma. Only one patient requiring intubation. Pool-related drowning were associated with a higher incidence of needing cardiopulmonary resuscitation (p = 0.02). The need for cardiopulmonary resuscitation (p = 0.05) and the occurrence of trauma (p = 0.02) were identified as risk factors for a longer hospitalisation. CONCLUSION: Prevention and early initiation of cardiopulmonary resuscitation are essential for achieving a favourable prognosis. Identifying demographic and environmental risk factors may help identify other effective preventive measures.

Correction: Surface alignment of ferroelectric nematic liquid crystals.

Correction for 'Surface alignment of ferroelectric nematic liquid crystals' by Federico Caimi et al., Soft Matter, 2021, 17, 8130-8139, https://doi.org/10.1039/D1SM00734C.

Characteristics of COVID-19 patients up to 6 months of age admitted to a paediatric emergency department.

Very young age could be a potential risk factor for community-acquired severe acute respiratory syndrome coronavirus 2, due to immature immune systems. We retrospectively enrolled 39 infants up to 6 months of age who had presented to our tertiary Italian children's hospital emergency room between 9 March 2020 and 8 March 2021 and tested positive for the virus. Of those, 38 had a non-specific mild or asymptomatic clinical course and only one patient was admitted to intensive care with severe symptoms. We concluded that very young infants with COVID-19 had a generally favourable disease course.

Needles in Haystacks: Understanding the Success of Selective Pairing of Nucleic Acids.

The effectiveness of several biological and biotechnological processes relies on the remarkably selective pairing of nucleic acids in contexts of molecular complexity. Relevant examples are the on-target binding of primers in genomic PCR and the regulatory efficacy of microRNA via binding on the transcriptome. Here, we propose a statistical framework that enables us to describe and understand such selectivity by means of a model that is extremely cheap from a computational point of view. By re-parametrizing the hybridization thermodynamics on three classes of base pairing errors, we find a convenient way to obtain the free energy of pairwise interactions between nucleic acids. We thus evaluate the hybridization statistics of a given oligonucleotide within a large number of competitive sites that we assume to be random, and we compute the probability of on-target binding. We apply our strategy to PCR amplification and microRNA-based gene regulation, shedding new light on their selectivity. In particular, we show the relevance of the defectless pairing of 3' terminals imposed by the polymerase in PCR selection. We also evaluate the selectivity afforded by the microRNA seed region, thus quantifying the extra contributions given by mechanisms beyond pairing statistics.

OxDNA to Study Species Interactions.

Molecular ecology uses molecular genetic data to answer traditional ecological questions in biogeography and biodiversity, among others. Several ecological principles, such as the niche hypothesis and the competitive exclusions, are based on the fact that species compete for resources. More in generally, it is now recognized that species interactions play a crucial role in determining the coexistence and abundance of species. However, experimentally controllable platforms, which allow us to study and measure competitions among species, are rare and difficult to implement. In this work, we suggest exploiting a Molecular Dynamics coarse-grained model to study interactions among single strands of DNA, representing individuals of different species, which compete for binding to other oligomers considered as resources. In particular, the well-established knowledge of DNA-DNA interactions at the nanoscale allows us to test the hypothesis that the maximum consecutive overlap between pairs of oligomers measure the species' competitive advantages. However, we suggest that a more complex structure also plays a role in the ability of the species to successfully bind to the target resource oligomer. We complement the simulations with experiments on populations of DNA strands which qualitatively confirm our hypotheses. These tools constitute a promising starting point for further developments concerning the study of controlled, DNA-based, artificial ecosystems.

Surface alignment of ferroelectric nematic liquid crystals.

The success of nematic liquid crystals in displays and optical applications is due to the combination of their optical uniaxiality, fluidity, elasticity, responsiveness to electric fields and controllable coupling of the molecular orientation at the interface with solid surfaces. The discovery of a polar nematic phase opens new possibilities for liquid crystal-based applications, but also requires a new study of how this phase couples with surfaces. Here we explore the surface alignment of the ferroelectric nematic phase by testing different rubbed and unrubbed substrates that differ in coupling strength and anchoring orientation and find a variety of behaviors - in terms of nematic orientation, topological defects and electric field response - that are specific to the ferroelectric nematic phase and can be understood as a consequence of the polar symmetry breaking. In particular, we show that by using rubbed polymer surfaces it is easy to produce cells with a planar polar preferential alignment and that cell electrostatics (e.g. grounding the electrodes) has a remarkable effect on the overall homogeneity of the ferroelectric ordering.

Yield stress "in a flash": investigation of nonlinearity and yielding in soft materials with an optofluidic microrheometer.

Yield stress materials deform as elastic solids or flow as viscous liquids, depending on the applied stress, which also allows them to trap particles below a certain size or density threshold. To investigate the conditions for such a transition at the microscale, we use an optofluidic microrheometer, based on the scattering of an infrared beam onto a microbead, which reaches forces in the nN scale. We perform creep experiments on a model soft material composed of swollen microgels, determining the limits of linear response and yield stress values, and observe quantitative agreement with bulk measurements. However, the motion of the microbead, both below and above yielding, reflects distinctive microscale features of the surrounding material, whose plastic rearrangements were investigated by us using small, passive tracers.