Clinical and prognostic significance of central and obstructive apneas in patients with transthyretin cardiac amyloidosis.

AIMS: Central (CA) and obstructive apneas (OA) are highly prevalent in patients with chronic heart failure (HF) and transthyretin cardiac amyloidosis (ATTR-CA) is an increasingly recognized HF etiology. This study aimed to investigate the prevalence and impact of CA and OA in patients with ATTR-CA. METHODS: Consecutive patients with ATTR-CA underwent a 24-hour ambulatory cardiorespiratory monitoring to evaluate the prevalence and severity of breathing disorders. The severity of these disorders was quantified using the apnea-hypopnea index (AHI). Accordingly, patients were categorized as having normal breathing (NB, AHI <5 events/hour), obstructive apnea (OA, AHI ≥5 events/hour with >50% being obstructive), or central apnea (CA, AHI >5 events/hour with ≥50% being central). The primary endpoint at follow-up was all-cause mortality. RESULTS: Out of 142 patients enrolled (n=142, aged 77±7 years, 91% males, 96% wild-type ATTR-CA), considering the 24 hours, 20% had NB (39% at daytime, 8% at nighttime), while 35% had CA (45% at daytime, 39% at nighttime) and 45% had OA (25% at daytime, 54% at nighttime). After a median 2.3 (1.4-3.3) years follow-up, 24-hour, daytime, and nighttime AHI were higher in non-survivors vs. survivors (all p<0.05), independently of the prevalent apnea type (p=0.64). At multivariable regression analysis (adjusted for the possible clinical, echocardiographic, and biohumoral confounders), nighttime AHI ≥30 events/hour (hazard ratio 2.37 [95%CI 1.07-5.23], p=0.033) and hs-troponin T (hazard ratio 2.43 [95%CI 1.42-4.17], p=0.001) were predictors of mortality. CONCLUSION: CA and OA are highly prevalent both at daytime and nighttime in patients with ATTR-CA and are associated with higher mortality.

This study investigated the prevalence and prognostic significance of central (CA) and obstructive apneas (OA) in 142 patients with transthyretin cardiac amyloidosis (ATTR-CA). Both CA and OA were highly prevalent during the whole 24-hour period, with only 20% classified as having normal breathing (meant as an apnea-hypopnea-index <5 events/hour during the 24-hour). OA were more frequent than CA, particularly during the night, while the prevalence of CA increased with worsening left ventricular systolic and diastolic dysfunction. At follow-up, 24-hour, daytime, and nighttime AHI were higher in non-survivors vs. survivors, independently of the prevalent apnea type and, at multivariable regression analysis (adjusted for the possible clinical, echocardiographic, and biohumoral confounders), nighttime AHI ≥30 events/hour was an independent predictor of mortality.

Integrating adult occurrence and reproduction data to identify conservation measures for amphibians.

Monitoring programs are pivotal to establishing sound management. Due to economic, logistic, and time limitations, monitoring programs often overlook differences among life-history stages. However, species occurrence does not necessarily mean population viability, and it is unclear to what extent monitoring programs that do not consider separately adult presence and reproduction provide effective management indications. Unfortunately, collecting data on certain life stages requires high sampling effort, leading to a trade-off between model reliability and resources needed for monitoring. We collected data on presence and reproduction of amphibians by monitoring 207 waterbodies in Lombardy (northern Italy) in 2017-2022. We then used multistate occupancy models to test whether certain environmental features, namely, pond area, hydroperiod, forest cover, shade, aquatic vegetation, and predators' presence, differentially affected adult occurrence and breeding probabilities of multiple amphibian species. To assess optimal sampling efforts, we modeled the detection probabilities of adults and reproduction across multiple species. Finally, we identified the optimal monitoring strategy under different scenarios of resource availability, comparing adult-only monitoring versus joint assessment of the occurrence of adults and reproduction. In many cases, the main drivers of adult occurrence and reproduction did not coincide because most investigated ecological variables affected one life stage or the other. Forest area, for instance, increased occurrence probabilities of adults of the endemic Rana latastei but showed no effect on their reproduction probabilities. Quantitative estimates of the sampling effort showed that occurrence of adults was easier to spot in 4 out of 7 species. Multicriteria decision analyses showed that when resources were scarce, monitoring adults was the optimal strategy for those 4 species. Conversely, with more resources, monitoring both adults and reproduction emerged as the best strategy for all the considered species. Integrated monitoring of adults and reproduction is essential to comprehensively identify effective conservation measures for amphibians.

Integración de datos de presencia adulta y de reproducción para identificar medidas de conservación para los anfibios Resumen Los programas de monitoreo son fundamentales para establecer una gestión adecuada. Debido a limitaciones económicas, logísticas y de tiempo, los programas de seguimiento suelen pasar por alto las diferencias entre las distintas fases del ciclo de vida. Sin embargo, la presencia de especies no significa necesariamente la viabilidad de la población, y no está claro hasta qué punto los programas de seguimiento que no consideran por separado la presencia de adultos y la reproducción proporcionan indicaciones eficaces para la gestión. Desgraciadamente, la recolección de datos sobre etapas determinadas del ciclo de vida requiere un gran esfuerzo de muestreo, lo que lleva a un compromiso entre la fiabilidad del modelo y los recursos necesarios para el seguimiento. Recopilamos datos sobre la presencia y reproducción de anfibios mediante el monitoreo de 207 cuerpos de agua en Lombardía (norte de Italia) entre 2017 y 2022. Después utilizamos modelos de ocupación multiestado para comprobar si determinadas características ambientales (superficie de los estanques, hidroperiodo, cubierta forestal, sombra, vegetación acuática y presencia de depredadores) afectaban de forma diferencial la presencia de adultos y a las probabilidades de reproducción de múltiples especies de anfibios. Para evaluar los esfuerzos de muestreo óptimos, modelamos las probabilidades de detección de adultos y reproducción de múltiples especies. Por último, identificamos la estrategia de seguimiento óptima en diferentes escenarios de disponibilidad de recursos y comparamos el seguimiento exclusivo de adultos frente a la evaluación conjunta de la presencia de adultos y reproducción. En muchos casos, los principales factores en la presencia de adultos y en la reproducción no coincidían, ya que la mayoría de las variables ecológicas investigadas afectaban a una u otra etapa del ciclo. La cubierta forestal, por ejemplo, aumentó la probabilidad de presencia de adultos de la especie endémica Rana latastei pero no mostraron un efecto sobre su probabilidad de reproducción. Las estimaciones cuantitativas del esfuerzo de muestreo mostraron que la presencia de adultos era más fácil de detectar en cuatro de las siete especies. Los análisis de decisión multicriterio mostraron que, cuando los recursos eran escasos, el seguimiento de los adultos era la estrategia óptima para esas cuatro especies. Por el contrario, con más recursos, el seguimiento tanto de los adultos como de la reproducción resultó ser la mejor estrategia para todas las especies consideradas. El seguimiento integrado de los adultos y la reproducción es esencial para identificar de forma exhaustiva medidas de conservación eficaces para los anfibios.

Treating heart failure by targeting the vagus nerve.

Increased sympathetic and reduced parasympathetic nerve activity is associated with disease progression and poor outcomes in patients with chronic heart failure. The demonstration that markers of autonomic imbalance and vagal dysfunction, such as reduced heart rate variability and baroreflex sensitivity, hold prognostic value in patients with chronic heart failure despite modern therapies encourages the research for neuromodulation strategies targeting the vagus nerve. However, the approaches tested so far have yielded inconclusive results. This review aims to summarize the current knowledge about the role of the parasympathetic nervous system in chronic heart failure, describing the pathophysiological background, the methods of assessment, and the rationale, limits, and future perspectives of parasympathetic stimulation either by drugs or bioelectronic devices.

The development of terrestrial ecosystems emerging after glacier retreat.

The global retreat of glaciers is dramatically altering mountain and high-latitude landscapes, with new ecosystems developing from apparently barren substrates1-4. The study of these emerging ecosystems is critical to understanding how climate change interacts with microhabitat and biotic communities and determines the future of ice-free terrains1,5. Here, using a comprehensive characterization of ecosystems (soil properties, microclimate, productivity and biodiversity by environmental DNA metabarcoding6) across 46 proglacial landscapes worldwide, we found that all the environmental properties change with time since glaciers retreated, and that temperature modulates the accumulation of soil nutrients. The richness of bacteria, fungi, plants and animals increases with time since deglaciation, but their temporal patterns differ. Microorganisms colonized most rapidly in the first decades after glacier retreat, whereas most macroorganisms took longer. Increased habitat suitability, growing complexity of biotic interactions and temporal colonization all contribute to the increase in biodiversity over time. These processes also modify community composition for all the groups of organisms. Plant communities show positive links with all other biodiversity components and have a key role in ecosystem development. These unifying patterns provide new insights into the early dynamics of deglaciated terrains and highlight the need for integrated surveillance of their multiple environmental properties5.

The problem of anthropogenic microfibres in karst systems: Assessment of water and submerged sediments.

A new worrying micropollutant threathens natural environments: the microfibres (MFs). Natural, regenerated and synthetic MFs have been detected in different environments, as well as in organisms. While synthetic MFs are generally detected in microplastic analyses, natural and regenerated MFs are not taken into account, or are wrongly considered plastics. They are generally considered biodegradable even if their degradation processes in ecosystems are poorly known. Their potential faster degradation could release toxic compounds, and their characteristics could led to a long-term accumulation in the environment. Understanding their dangerousness and the possible impact they could have on ecosystems is fundamental for environment conservation. We collected and investigated water and submerged sediment samples in different caves and springs of the Classical Karst Region (NE Italy), rich in protected habitats and species. MFs were analysed via microscopy and spectroscopy. MFs were found in all samples, highlighting pollution in surface and subterranean habitats of the karst system. MF concentration was higher in submerged sediments respect to waters, highlighting an accumulation of MFs over time. Big microfibres were less abundant, and MF amount increased with the decrease in the considered size. More than 80% of fibres were fluorescent under UV light. Fluorescent MFs were especially transparent, while non-fluorescent ones were mainly black and blue. Most MFs were cellulosic, and synthetic MFs represent only 15-22%, highlighting a significant gap between the MF composition detected in natural environments and the global production of synthetic textiles in recent times. Synthetic MFs were more abundant in waters. Our results improve the knowledge on micropollutants in karst environments, laying the foundations for future research. MF pollution monitoring in karst areas must become a priority for species protection, habitat conservation, and waters management, improving analyses on a larger number of aquatic environments, taking into account the ecological connections between surface and subterranean habitats.

Eligibility for vericiguat in a real-world, contemporary heart failure population.

AIMS: Vericiguat is a soluble guanylate cyclase stimulator and improves survival in patients with heart failure (HF) with reduced ejection fraction (HFrEF) and an increased risk of decompensation. As real-world data on how many patients could be eligible for vericiguat therapy derive from outdated registries, we aimed to assess eligibility in a prospective cohort of patients with HF. METHODS AND RESULTS: Data from consecutive HF patients undergoing an elective ambulatory visit at five university hospitals from 3 July to 28 July 2023 were collected. Independent investigators assessed which patients (i) met the eligibility criteria of the VICTORIA trial, (ii) complied with HF guideline recommendations, (iii) met regulatory agency criteria, or (iv) met criteria for refundability according to the Italian regulatory agency. Patients (n = 346, 72% men, median age 69 years) had HFrEF in 57% of cases, left ventricular ejection fraction < 45% in 68%, and New York Heart Association class II-IV symptoms in 76%. Patients meeting the eligibility criteria of the VICTORIA trial or European and American HF Guideline recommendations were 9% and 13%, respectively. Patients meeting Food and Drug Administration (FDA) or European Medicines Agency (EMA) label criteria were 19% and 17%, respectively. Drug costs would be covered by the Italian National Health System in 10% of patients [if a sodium-glucose cotransporter-2 inhibitor (SGLT2i) is not mandatory] or in 8% (if an SGLT2i is requested). CONCLUSIONS: In a real-world study, 9% of patients met the eligibility criteria of the VICTORIA trial, but up to 13% complied with guideline recommendations and up to 19% met FDA or EMA criteria. In Italy, drug costs would be covered by up to 10% of patients.

Echocardiography-Derived Forward Left Ventricular Output Improves Risk Prediction in Systolic Heart Failure.

BACKGROUND: Although it is widely used to classify patients with heart failure (HF), the prognostic role of left ventricular ejection fraction (LVEF) is debated. The aim of this study was to test the hypothesis that echocardiographic measures of forward left ventricular (LV) output, being more representative of cardiac hemodynamics, might improve risk prediction in a large cohort of patients with HF with systolic dysfunction. METHODS: Consecutive stable patients with HF with LVEF <50% on guideline-recommended therapies undergoing echocardiography including the evaluation of forward LV output (i.e., LV outflow tract [LVOT] velocity-time integral [VTI], stroke volume index [SVi], and cardiac index) over a 6-year period were selected and followed for the end point of cardiac and all-cause death. RESULTS: Among the 1,509 patients analyzed (mean age, 71 ± 12 years; 75% men; mean LVEF, 35 ± 9%), 328 (22%) died during a median follow-up period of 28 months (interquartile range, 14-40 months), 165 (11%) of cardiac causes. On multivariable regression analysis, LVOT VTI (P < .001), SVi (P < .001), and cardiac index (P < .001), but not LVEF (P > .05), predicted cardiac and all-cause death. The optimal prognostic cutoffs for LVOT VTI, SVi, and cardiac index were 15 cm, 38 mL/m2, and 2 L/min/m2, respectively. Adding each of these measures to a multivariable risk model (including clinical, biohumoral, and echocardiographic markers) improved risk prediction (P < .001). Among the different measures of forward LV output, cardiac index was less accurate than LVOT VTI and SVi. CONCLUSIONS: The echocardiographic evaluation of forward LV output improves risk prediction in patients with HF across a wide LVEF spectrum over other well-established clinical, biohumoral, and echocardiographic prognostic markers.

Association of APOE genotype and cerebrospinal fluid Aß and tau biomarkers with cognitive and motor phenotype in amyotrophic lateral sclerosis.

OBJECTIVE: Little is known about amyotrophic lateral sclerosis (ALS)-nonspecific cognitive deficits - most notably memory disturbance - and their biological underpinnings. We investigated the associations of the Alzheimer's disease (AD) genetic risk factor APOE and cerebrospinal fluid (CSF) biomarkers Aß and tau proteins with cognitive and motor phenotype in ALS. METHODS: APOE haplotype was determined in 281 ALS patients; for 105 of these, CSF levels of Aß42, Aß40, total tau (T-tau), and phosphorylated tau (P-tau181) were quantified by chemiluminescence enzyme immunoassay (CLEIA). The Edinburgh Cognitive and Behavioural ALS Screen (ECAS) was employed to evaluate the neuropsychological phenotype. RESULTS: APOE-E4 allele was associated with worse ECAS memory score (median, 14.0 in carriers vs. 16.0 in non-carriers) and lower CSF Aß42 (-0.8 vs. 0.1, log-transformed values) and Aß42/40 ratio (-0.1 vs. 0.3). Some 37.1% of ALS patients showed low Aß42 levels, possibly reflecting cerebral Aß deposition. While lower Aß42/40 correlated with lower memory score (ß = 0.20), Aß42 positively correlated with both ALS-specific (ß = 0.24) and ALS-nonspecific (ß = 0.24) scores. Although Aß42/40 negatively correlated with T-tau (ß = -0.29) and P-tau181 (ß = -0.33), we found an unexpected positive association of Aß42 and Aß40 with both tau proteins. Regarding motor phenotype, lower levels of Aß species were associated with lower motor neuron (LMN) signs (Aß40: ß = 0.34; Aß42: ß = 0.22). CONCLUSIONS: APOE haplotype and CSF Aß biomarkers are associated with cognitive deficits in ALS and particularly with memory impairment. This might partly reflect AD-like pathophysiological processes, but additional ALS-specific mechanisms could be involved.

Risk of peripheral neuropathy in patients with psoriasis and psoriatic arthritis. A prospective cohort study.

INTRODUCTION/AIMS: Laboratory and clinical data suggest a link between neurologically mediated inflammation and psoriasis, but the risk and features of peripheral neuropathy in psoriasis or psoriatic arthritis remain unknown. The aim of this exploratory study was to evaluate the risk and to describe the features of peripheral neuropathy in patients with psoriasis and psoriatic arthritis. METHODS: One hundred patients with psoriasis and/or psoriatic arthritis and 100 control subjects were consecutively enrolled. Diagnostic confirmation included electrophysiological examination, skin biopsy, and nerve ultrasound for confirmed polyneuropathy. RESULTS: Nine patients were diagnosed with confirmed polyneuropathy, while none of the control subjects had the condition (relative risk [RR] = 19.00, 95% confidence interval [CI] = 1.12-322.11). Specific relative risks for polyneuropathy were 22.09 (95% CI = 1.17-416.43) in psoriasis patients and 18.75 (95% CI = 1.07-327.62) in psoriatic arthritis patients. The observed polyneuropathy in all nine patients was length-dependent, symmetrical, and predominantly sensory, with minimal or no disability. Comorbidities and exposure to therapies known to increase the risk of polyneuropathy were more frequent in psoriasis and/or psoriatic arthritis patients compared to controls (42% vs. 4%, p = .0001). Analyzing data after excluding possible contributory causes, the risk of polyneuropathy in patients with psoriasis and/or psoriatic arthritis was not significant. DISCUSSION: Psoriasis and psoriatic arthritis appear to be associated with an increased risk of polyneuropathy. This increased risk seems to be linked to the higher prevalence of contributing factors for polyneuropathy, rather than a direct increase in neuropathy risk specifically related to psoriasis and psoriatic arthritis.

Four years monitoring of the endangered European plethodontid salamanders.

The ongoing biodiversity crisis is strongly threatening amphibians, mostly because of their peculiar physiology, their sensitivity to climate change and the spread of diseases. Effective monitoring involving assessments of pressure effects across time and estimation of population trends play a key role in mitigating amphibian decline. To improve implementation of standardized protocols and conservation efforts, we present here a dataset related to one of the amphibian genera whose onservation status is considered the most declining according to the IUCN. We report information on 66 populations of the endangered European cave salamanders, genus Speleomantes, that was collected through a standardized monitoring along a four-year period (2021-2024). Demographics data of the populations and fitness-related data of single individuals are reported. Furthermore, we include 3,836 high quality images of individuals that can allow to perform studies aiming to assess the phenotypic variability within the genus, and to perform long-term capture-mark-recaptured studies.

In silico screening of LRRK2 WDR domain inhibitors using deep docking and free energy simulations.

The Critical Assessment of Computational Hit-Finding Experiments (CACHE) Challenge series is focused on identifying small molecule inhibitors of protein targets using computational methods. Each challenge contains two phases, hit-finding and follow-up optimization, each of which is followed by experimental validation of the computational predictions. For the CACHE Challenge #1, the Leucine-Rich Repeat Kinase 2 (LRRK2) WD40 Repeat (WDR) domain was selected as the target for in silico hit-finding and optimization. Mutations in LRRK2 are the most common genetic cause of the familial form of Parkinson's disease. The LRRK2 WDR domain is an understudied drug target with no known molecular inhibitors. Herein we detail the first phase of our winning submission to the CACHE Challenge #1. We developed a framework for the high-throughput structure-based virtual screening of a chemically diverse small molecule space. Hit identification was performed using the large-scale Deep Docking (DD) protocol followed by absolute binding free energy (ABFE) simulations. ABFEs were computed using an automated molecular dynamics (MD)-based thermodynamic integration (TI) approach. 4.1 billion ligands from Enamine REAL were screened with DD followed by ABFEs computed by MD TI for 793 ligands. 76 ligands were prioritized for experimental validation, with 59 compounds successfully synthesized and 5 compounds identified as hits, yielding a 8.5% hit rate. Our results demonstrate the efficacy of the combined DD and ABFE approaches for hit identification for a target with no previously known hits. This approach is widely applicable for the efficient screening of ultra-large chemical libraries as well as rigorous protein-ligand binding affinity estimation leveraging modern computational resources.

Bisphenol A affects the development and the onset of photosymbiosis in the acoel Symsagittiferaroscoffensis.

Photosymbiosis indicates a long-term association between animals and photosynthetic organisms. It has been mainly investigated in photosymbiotic cnidarians, while other photosymbiotic associations have been largely neglected. The acoel Symsagittifera roscoffensis lives in obligatory symbiosis with the microalgal Tetraselmis convolutae and has recently emerged as alternative model to study photosymbiosis. Here, we investigated the effects of Bisphenol A, a common plastic additive, on two pivotal stages of its lifecycle: aposymbiotic juvenile development and photosymbiogenesis. Based on our results, this pollutant altered the development of the worms and their capacity to engulf algae from the environment at concentrations higher than the levels detected in seawater, yet aligning with those documented in sediments of populated areas. Data provide novel information about the effects of pollutants on photosymbiotic associations and prompt the necessity to monitor their concentrations in marine environmental matrices.

An open computational toolbox to analyze multi- and single-unit sympathetic nerve activity in microneurography.

Microelectrode recordings from human peripheral and cranial nerves provide a means to study both afferent and efferent axonal signals at different levels of detail, from multi- to single-unit activity. Their analysis can lead to advancements both in diagnostic and in the understanding of the genesis of neural disorders. However, most of the existing computational toolboxes for the analysis of microneurographic recordings are limited in scope or not open-source. Additionally, conventional burst-based metrics are not suited to analyze pathological conditions and are highly sensitive to distance of the microelectrode tip from the active axons. To address these challenges, we developed an open-source toolbox that offers advanced analysis capabilities for studying neuronal reflexes and physiological responses to peripheral nerve activity. Our toolbox leverages the observation of temporal sequences of action potentials within inherently cyclic signals, introducing innovative methods and indices to enhance analysis accuracy. Importantly, we have designed our computational toolbox to be accessible to novices in biomedical signal processing. This may include researchers and professionals in healthcare domains, such as clinical medicine, life sciences, and related fields. By prioritizing user-friendliness, our software application serves as a valuable resource for the scientific community, allowing to extract advanced metrics of neural activity in short time and evaluate their impact on other physiological variables in a consistent and standardized manner, with the final aim to widen the use of microneurography among researchers and clinicians.

The role of elasticity on adhesion and clustering of neurons on soft surfaces.

The question of whether material stiffness enhances cell adhesion and clustering is still open to debate. Results from the literature are seemingly contradictory, with some reports illustrating that adhesion increases with surface stiffness and others suggesting that the performance of a system of cells is curbed by high values of elasticity. To address the role of elasticity as a regulator in neuronal cell adhesion and clustering, we investigated the topological characteristics of networks of neurons on polydimethylsiloxane (PDMS) surfaces - with values of elasticity (E) varying in the 0.55-2.65 MPa range. Results illustrate that, as elasticity increases, the number of neurons adhering on the surface decreases. Notably, the small-world coefficient - a topological measure of networks - also decreases. Numerical simulations and functional multi-calcium imaging experiments further indicated that the activity of neuronal cells on soft surfaces improves for decreasing E. Experimental findings are supported by a mathematical model, that explains adhesion and clustering of cells on soft materials as a function of few parameters - including the Young's modulus and roughness of the material. Overall, results indicate that - in the considered elasticity interval - increasing the compliance of a material improves adhesion, improves clustering, and enhances communication of neurons.

Alpine salamanders at risk? The current status of an emerging fungal pathogen.

Amphibians globally suffer from emerging infectious diseases like chytridiomycosis caused by the continuously spreading chytrid fungi. One is Batrachochytrium salamandrivorans (Bsal) and its disease ‒ the 'salamander plague' ‒ which is lethal to several caudate taxa. Recently introduced into Western Europe, long distance dispersal of Bsal, likely through human mediation, has been reported. Herein we study if Alpine salamanders (Salamandra atra and S. lanzai) are yet affected by the salamander plague in the wild. Members of the genus Salamandra are highly susceptible to Bsal leading to the lethal disease. Moreover, ecological modelling has shown that the Alps and Dinarides, where Alpine salamanders occur, are generally suitable for Bsal. We analysed skin swabs of 818 individuals of Alpine salamanders and syntopic amphibians at 40 sites between 2017 to 2022. Further, we compiled those with published data from 319 individuals from 13 sites concluding that Bsal infections were not detected. Our results suggest that the salamander plague so far is absent from the geographic ranges of Alpine salamanders. That means that there is still a chance to timely implement surveillance strategies. Among others, we recommend prevention measures, citizen science approaches, and ex situ conservation breeding of endemic salamandrid lineages.

Biochemical properties of chromatin domains define genome compartmentalization.

Chromatin three-dimensional (3D) organization inside the cell nucleus determines the separation of euchromatin and heterochromatin domains. Their segregation results in the definition of active and inactive chromatin compartments, whereby the local concentration of associated proteins, RNA and DNA results in the formation of distinct subnuclear structures. Thus, chromatin domains spatially confined in a specific 3D nuclear compartment are expected to share similar epigenetic features and biochemical properties, in terms of accessibility and solubility. Based on this rationale, we developed the 4f-SAMMY-seq to map euchromatin and heterochromatin based on their accessibility and solubility, starting from as little as 10 000 cells. Adopting a tailored bioinformatic data analysis approach we reconstruct also their 3D segregation in active and inactive chromatin compartments and sub-compartments, thus recapitulating the characteristic properties of distinct chromatin states. A key novelty of the new method is the capability to map both the linear segmentation of open and closed chromatin domains, as well as their compartmentalization in one single experiment.

Transient social-ecological dynamics reveal signals of decoupling in a highly disturbed Anthropocene landscape.

Understanding the transient dynamics of interlinked social-ecological systems (SES) is imperative for assessing sustainability in the Anthropocene. However, how to identify critical transitions in real-world SES remains a formidable challenge. In this study, we present an evolutionary framework to characterize these dynamics over an extended historical timeline. Our approach leverages multidecadal rates of change in socioeconomic data, paleoenvironmental, and cutting-edge sedimentary ancient DNA records from China's Yangtze River Delta, one of the most densely populated and intensively modified landscapes on Earth. Our analysis reveals two significant social-ecological transitions characterized by contrasting interactions and feedback spanning several centuries. Initially, the regional SES exhibited a loosely connected and ecologically sustainable regime. Nevertheless, starting in the 1950s, an increasingly interconnected regime emerged, ultimately resulting in the crossing of tipping points and an unprecedented acceleration in soil erosion, water eutrophication, and ecosystem degradation. Remarkably, the second transition occurring around the 2000s, featured a notable decoupling of socioeconomic development from ecoenvironmental degradation. This decoupling phenomenon signifies a more desirable reconfiguration of the regional SES, furnishing essential insights not only for the Yangtze River Basin but also for regions worldwide grappling with similar sustainability challenges. Our extensive multidecadal empirical investigation underscores the value of coevolutionary approaches in understanding and addressing social-ecological system dynamics.

In silico assessment of 18S rDNA metabarcoding markers for the characterization of nematode communities.

Nematodes are keystone actors of soil, freshwater and marine ecosystems, but the complexity of morphological identification has limited broad-scale monitoring of nematode biodiversity. DNA metabarcoding is increasingly used to assess nematode diversity but requires universal primers with high taxonomic coverage and high taxonomic resolution. Several primers have been proposed for the metabarcoding of nematode diversity, many of which target the 18S rRNA gene. In silico analyses have a great potential to assess key parameters of primers, including taxonomic coverage, resolution and specificity. Based on a recently-available reference database, we tested in silico the performance of fourteen commonly used and one newly optimized primer for nematode metabarcoding. Most primers showed very good coverage, amplifying most of the sequences in the reference database, while four markers showed limited coverage. All primers showed good taxonomic resolution. Resolution was particularly good if the aim was the identification of higher-level taxa, such as genera or families. Overall, species-level resolution was higher for primers amplifying long fragments. None of the primers was highly specific for nematodes as, despite some variation, they all amplified a large number of other eukaryotes. Differences in performance across primers highlight the complexity of the choice of markers appropriate for the metabarcoding of nematodes, which depends on a trade-off between taxonomic resolution and the length of amplified fragments. Our in silico analyses provide new insights for the identification of the most appropriate primers, depending on the study goals and the origin of DNA samples. This represents an essential step to design and optimize metabarcoding studies assessing nematode diversity.