How microscopic epistasis and clonal interference shape the fitness trajectory in a spin glass model of microbial long-term evolution

The adaptive dynamics of evolving microbial populations takes place on a complex fitness landscape generated by epistatic interactions. The population generically consists of multiple competing strains, a phenomenon known as clonal interference. Microscopic epistasis and clonal interference are central aspects of evolution in microbes, but their combined effects on the functional form of the population's mean fitness are poorly understood. Here, we develop a computational method that resolves the full microscopic complexity of a simulated evolving population subject to a standard serial dilution protocol. Through extensive numerical experimentation, we find that stronger microscopic epistasis gives rise to fitness trajectories with slower growth independent of the number of competing strains, which we quantify with power-law fits and understand mechanistically via a random walk model that neglects dynamical correlations between genes. We show that increasing the level of clonal interference leads to fitness trajectories with faster growth (in functional form) without microscopic epistasis, but leaves the rate of growth invariant when epistasis is sufficiently strong, indicating that the role of clonal interference depends intimately on the underlying fitness landscape. The simulation package for this work may be found at https://github.com/nmboffi/spin_glass_evodyn.

Persistent Exhausted T-Cell Immunity after Severe COVID-19: 6-Month Evaluation in a Prospective Observational Study

INTRODUCTION

Severe COVID-19 can result in a significant and irreversible impact on long-term recovery and subsequent immune protection. Understanding the complex immune reactions may be useful for establishing clinically relevant monitoring.

METHODS

Hospitalized adults with SARS-CoV-2 between March/October 2020 (n = 64) were selected. Cryopreserved peripheral blood mononuclear cells (PBMCs) and plasma samples were obtained at hospitalization (baseline) and 6 months after recovery. Immunological components' phenotyping and SARS-CoV-2-specific T-cell response were studied in PBMCs by flow cytometry. Up to 25 plasma pro/anti-inflammatory cytokines/chemokines were assessed by LEGENDplex immunoassays. The SARS-CoV-2 group was compared to matched healthy donors.

RESULTS

Biochemical altered parameters during infection were normalized at a follow-up time point in the SARS-CoV-2 group. Most of the cytokine/chemokine levels were increased at baseline in the SARS-CoV-2 group. This group showed increased Natural Killer cells (NK) activation and decreased CD16^high NK subset, which normalized six months later. They also presented a higher intermediate and patrolling monocyte proportion at baseline. T cells showed an increased terminally differentiated (TemRA) and effector memory (EM) subsets distribution in the SARS-CoV-2 group at baseline and continued to increase six months later. Interestingly, T-cell activation (CD38) in this group decreased at the follow-up time point, contrary to exhaustion markers (TIM3/PD1). In addition, we observed the highest SARS-CoV-2-specific T-cell magnitude response in TemRA CD4 T-cell and EM CD8 T-cell subsets at the six-months time point.

CONCLUSIONS

The immunological activation in the SARS-CoV-2 group during hospitalization is reversed at the follow-up time point. However, the marked exhaustion pattern remains over time. This dysregulation could constitute a risk factor for reinfection and the development of other pathologies. Additionally, high SARS-CoV-2-specific T-cells response levels appear to be associated with infection severity.

No Alteration Between Intrinsic Connectivity Networks by a Pilot Study on Localized Exposure to the Fourth-Generation Wireless Communication Signals

Neurophysiological effect of human exposure to radiofrequency signals has attracted considerable attention, which was claimed to have an association with a series of clinical symptoms. A few investigations have been conducted on alteration of brain functions, yet no known research focused on intrinsic connectivity networks, an attribute that may relate to some behavioral functions. To investigate the exposure effect on functional connectivity between intrinsic connectivity networks, we conducted experiments with seventeen participants experiencing localized head exposure to real and sham time-division long-term evolution signal for 30 min. The resting-state functional magnetic resonance imaging data were collected before and after exposure, respectively. Group-level independent component analysis was used to decompose networks of interest. Three states were clustered, which can reflect different cognitive conditions. Dynamic connectivity as well as conventional connectivity between networks per state were computed and followed by paired sample t-tests. Results showed that there was no statistical difference in static or dynamic functional network connectivity in both real and sham exposure conditions, and pointed out that the impact of short-term electromagnetic exposure was undetected at the ICNs level. The specific brain parcellations and metrics used in the study may lead to different results on brain modulation.

Factors Influencing the Evolution of Pulmonary Hypertension in Previously Healthy Subjects Recovering from a SARS-CoV-2 Infection

(1) Background: While the COVID-19 pandemic has been persisting for almost 2 years, more and more people are diagnosed with residual complications such as pulmonary hypertension (PH) and right ventricular dysfunction (RVD). This study aims to evaluate the course of PH and borderline PH (BPH) at 3 and 6 months after the acute COVID-19 infection and investigate if there are differences regarding its evolution between the patients from the first three waves of this disease. (2) Methods: We analyzed, by transthoracic echocardiography (TTE), the 3 and 6 months' evolution of the echocardiographically estimated systolic pulmonary artery pressures (esPAP) in 116 patients already diagnosed with PH or BPH due to COVID-19 during the first three subsequent waves of COVID-19. (3) Results: We documented a gradual, statistically significant reduction in esPAP values, but also an improvement of the parameters characterizing RVD after 3 and 6 months (p < 0.001). This evolution was somewhat different between subjects infected with different viral strains and was related to the initial severity of the pulmonary injury and PH (adjusted R² = 0.722, p < 0.001). (4) Conclusions: PH and RVD alleviate gradually during the recovery after COVID-19, but in some cases, they persist, suggesting the activation of pathophysiological mechanisms responsible for the self-propagation of PH.

Childhood epilepsy with a small number of seizures may be left untreated: an international prospective study

It is unknown whether treatment with antiepileptic drugs in children with epilepsy with a presumed good prognosis is always necessary. We aimed to study the course of newly diagnosed epilepsy in children with a presumed good prognosis who are managed without AED treatment. A total of 151 children (one month to 12 years of age) with two to five lifetime unprovoked seizures (excluding febrile convulsions), were followed for three years. Treatment was initially withheld. Children with symptomatic epilepsy, or absence or myoclonic epilepsy, were excluded. AED treatment was started after >10 lifetime seizures or an episode of status epilepticus during follow-up, or if the parents or treating physician deemed it otherwise necessary. During follow-up, 113 children continued to meet our criteria for refraining from treatment with antiepileptic drugs, yet 30 started treatment at the request of the parents. Thirty-eight children at some time met the criteria to start treatment, but the parents of 16 declined treatment. In all, 99 (66%) children maintained the no-treatment regime. Ninety-eight children (65% of 151) reached terminal remission for at least one year, including 83 who did not receive antiepileptic drug treatment (84% of the untreated 99). Mean terminal remission was significantly longer in the group with a total of <10 seizures compared to those with >10 seizures. Treatment did not increase the length of terminal remission. Adverse events, including traumatic injury, occurred equally in the treated and untreated children. Measures of quality of life suggested a better outcome in those without treatment. Children with newly diagnosed epilepsy with a presumed good prognosis may not need immediate AED treatment. Postponing treatment does not alter the chance of remission or the risk of accidents and adverse events and appears to be associated with a good quality of life.

A common evolutionary pathway for maintaining quorum sensing in Pseudomonas aeruginosa

In the bacterium Pseudomonas aeruginosa, the synthesis and secretion of extracellular protease is a typical cooperative behavior regulated by quorum sensing. However, this type of cooperative behavior is easily exploited by other individuals who do not synthesize public goods, which is known as the "tragedy of the commons". Here P. aeruginosa was inoculated into casein media with different nitrogen salts added. In casein broth, protease (a type of public good) is necessary for bacterial growth. After 30 days of sequential transfer, some groups propagated stably and avoided "tragedy of the commons". The evolved cooperators who continued to synthesize protease were isolated from these stable groups. By comparing the characteristics of quorum sensing in these cooperators, an identical evolutionary pattern was found. A variety of cooperative behaviors regulated by quorum sensing, such as the synthesis and secretion of protease and signals, were significantly reduced during the process of evolution. Such reductions improved the efficiency of cooperation, helping to prevent cheating. In addition, the production of pyocyanin, which is regulated by the RhlIR system, increased during the process of evolution, possibly due to its role in stabilizing the cooperation. This study contributes towards our understanding of the evolution of quorum sensing of P. aeruginosa.

Long-Term Evolution Electromagnetic Fields Exposure Modulates the Resting State EEG on Alpha and Beta Bands

Long-term evolution (LTE) wireless telecommunication systems are widely used globally, which has raised a concern that exposure to electromagnetic fields (EMF) emitted from LTE devices can change human neural function. To date, few studies have been conducted on the effect of exposure to LTE EMF. Here, we evaluated the changes in electroencephalogram (EEG) due to LTE EMF exposure. An LTE EMF exposure system with a stable power emission, which was equivalent to the maximum emission from an LTE mobile phone, was used to radiate the subjects. Numerical simulations were conducted to ensure that the specific absorption rate in the subject's head was below the safety limits. Exposure to LTE EMF reduced the spectral power and the interhemispheric coherence in the alpha and beta bands of the frontal and temporal brain regions. No significant change was observed in the spectral power and the inter-hemispheric coherence in different timeslots during and after the exposure. These findings also corroborated those of our previous study using functional magnetic resonant imaging.

Diversity and Coevolutionary Dynamics in High-Dimensional Phenotype Spaces

We study macroevolutionary dynamics by extending microevolutionary competition models to long timescales. It has been shown that for a general class of competition models, gradual evolutionary change in continuous phenotypes (evolutionary dynamics) can be nonstationary and even chaotic when the dimension of the phenotype space in which the evolutionary dynamics unfold is high. It has also been shown that evolutionary diversification can occur along nonequilibrium trajectories in phenotype space. We combine these lines of thinking by studying long-term coevolutionary dynamics of emerging lineages in multidimensional phenotype spaces. We use a statistical approach to investigate the evolutionary dynamics of many different systems. We find (1) that, for a given dimension of phenotype space, the coevolutionary dynamics tend to be fast and nonstationary for an intermediate number of coexisting lineages but tend to stabilize as the evolving communities reach a saturation level of diversity and (2) that the amount of diversity at the saturation level increases rapidly (exponentially) with the dimension of phenotype space. These results have implications for theoretical perspectives on major macroevolutionary patterns such as adaptive radiation, long-term temporal patterns of phenotypic changes, and the evolution of diversity.

Cardiac ultrasonography over 4G wireless networks using a tele-operated robot

This Letter proposes an end-to-end mobile tele-echography platform using a portable robot for remote cardiac ultrasonography. Performance evaluation investigates the capacity of long-term evolution (LTE) wireless networks to facilitate responsive robot tele-manipulation and real-time ultrasound video streaming that qualifies for clinical practice. Within this context, a thorough video coding standards comparison for cardiac ultrasound applications is performed, using a data set of ten ultrasound videos. Both objective and subjective (clinical) video quality assessment demonstrate that H.264/AVC and high efficiency video coding standards can achieve diagnostically-lossless video quality at bitrates well within the LTE supported data rates. Most importantly, reduced latencies experienced throughout the live tele-echography sessions allow the medical expert to remotely operate the robot in a responsive manner, using the wirelessly communicated cardiac ultrasound video to reach a diagnosis. Based on preliminary results documented in this Letter, the proposed robotised tele-echography platform can provide for reliable, remote diagnosis, achieving comparable quality of experience levels with in-hospital ultrasound examinations.

Evolution of high mobility group nucleosome-binding proteins and its implications for vertebrate chromatin specialization

High mobility group (HMG)-N proteins are a family of small nonhistone proteins that bind to nucleosomes (N). Despite the amount of information available on their structure and function, there is an almost complete lack of information on the molecular evolutionary mechanisms leading to their exclusive differentiation. In the present work, we provide evidence suggesting that HMGN lineages constitute independent monophyletic groups derived from a common ancestor prior to the diversification of vertebrates. Based on observations of the functional diversification across vertebrate HMGN proteins and on the extensive silent nucleotide divergence, our results suggest that the long-term evolution of HMGNs occurs under strong purifying selection, resulting from the lineage-specific functional constraints of their different protein domains. Selection analyses on independent lineages suggest that their functional specialization was mediated by bursts of adaptive selection at specific evolutionary times, in a small subset of codons with functional relevance-most notably in HMGN1, and in the rapidly evolving HMGN5. This work provides useful information to our understanding of the specialization imparted on chromatin metabolism by HMGNs, especially on the evolutionary mechanisms underlying their functional differentiation in vertebrates.