Publisher Correction: The tuatara genome reveals ancient features of amniote evolution.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The tuatara genome reveals ancient features of amniote evolution.

The tuatara (Sphenodon punctatus)-the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana1,2-is an iconic species that is endemic to New Zealand2,3. A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes2,4. Here we analyse the genome of the tuatara, which-at approximately 5 Gb-is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features. The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. Our study also provides important insights into both the technical challenges and the cultural obligations that are associated with genome sequencing.

Monolayer-to-Mesoscale Modulation of the Optical Properties in 2D CrI_{3} Mapped by Hyperspectral Microscopy.

Magnetic 2D materials hold promise to change the miniaturization paradigm of unidirectional photonic components. However, the integration of these materials in devices hinges on the accurate determination of the optical properties down to the monolayer limit, which is still missing. By using hyperspectral wide-field imaging at room temperature, we reveal a nonmonotonic thickness dependence of the complex optical dielectric function in the archetypal magnetic 2D material CrI_{3} extending across different length scales: onsetting at the mesoscale, peaking at the nanoscale, and decreasing again down to the single layer. These results portray a modification of the electronic properties of the material and align with the layer-dependent magnetism in CrI_{3}, shedding light on the long-standing structural conundrum in this material. The unique modulation of the complex dielectric function from the monolayer up to more than 100 layers will be instrumental for understanding mesoscopic effects in layered materials and tuning light-matter interactions in magnetic 2D materials.

Analysis of microsamples by miniaturized magnetic-based pipette tip microextraction: determination of free cortisol in serum and urine from very low birth weight preterm newborns.

Miniaturized magnetic-based pipette tip microextraction is presented as a sample preparation approach for microsamples. It involves quick dispersion of a diminutive amount of a magnetic sorbent material in a low-volume sample (10 µL) to entrap the target analytes. Next, the dispersion is aspirated using a (semi)automatic pipette through a pipette tip with a small cubic neodymium magnet inside, which retrieves the magnetic sorbent containing the analytes. After discarding the rest of the sample, the sorbent is properly rinsed by aspirating/dispensing deionized water, and then, the analytes are eluted by aspirating/dispensing an appropriate solvent. This approach was employed for the determination of free cortisol in serum and urine from very low birth weight preterm newborns, a vulnerable patient group who present low availability for sampling biological fluids. A magnetic immunosorbent made of a cortisol antibody was employed for the selective extraction, followed by liquid chromatography-tandem mass spectrometry. Good analytical features were obtained, such as limits of detection and quantification of 0.08 and 0.27 ng mL-1, respectively, linearity up to 50 ng mL-1 (R2 > 0.999), RSD values under 15% and relative recoveries between 91 and 111%. The cross-reactivity with other glucocorticoids (i.e., cortisone and prednisolone) was evaluated to show the selectivity of the extraction. Finally, the method applicability was demonstrated towards the determination of free cortisol in the serum and urine samples from low birth weight preterm newborns.

Biphasic concentration patterns in ionic transport under nanoconfinement revealed in steady-state and time-dependent properties.

Ion permeation across nanoscopic structures differs considerably from microfluidics because of strong steric constraints, transformed solvent properties, and charge-regulation effects revealed mostly in diluted solutions. However, little is known about nanofluidics in moderately concentrated solutions, which are critically important for industrial applications and living systems. Here, we show that nanoconfinement triggers general biphasic concentration patterns in a myriad of ion transport properties by using two contrasting systems: a biological ion channel and a much larger synthetic nanopore. Our findings show a low-concentration regime ruled by classical Debye screening and another one where ion-ion correlations and enhanced ion-surface interactions contribute differently to each electrophysiological property. Thus, different quantities (e.g., conductance vs noise) measured under the same conditions may appear contradictory because they belong to different concentration regimes. In addition, non-linear effects that are barely visible in bulk conductivity only in extremely concentrated solutions become apparent in nanochannels around physiological conditions.

Ecological Specialization and Evolutionary Reticulation in Extant Hyaenidae.

During the Miocene, Hyaenidae was a highly diverse family of Carnivora that has since been severely reduced to four species: the bone-cracking spotted, striped, and brown hyenas, and the specialized insectivorous aardwolf. Previous studies investigated the evolutionary histories of the spotted and brown hyenas, but little is known about the remaining two species. Moreover, the genomic underpinnings of scavenging and insectivory, defining traits of the extant species, remain elusive. Here, we generated an aardwolf genome and analyzed it together with the remaining three species to reveal their evolutionary relationships, genomic underpinnings of their scavenging and insectivorous lifestyles, and their respective genetic diversities and demographic histories. High levels of phylogenetic discordance suggest gene flow between the aardwolf lineage and the ancestral brown/striped hyena lineage. Genes related to immunity and digestion in the bone-cracking hyenas and craniofacial development in the aardwolf showed the strongest signals of selection, suggesting putative key adaptations to carrion and termite feeding, respectively. A family-wide expansion in olfactory receptor genes suggests that an acute sense of smell was a key early adaptation. Finally, we report very low levels of genetic diversity within the brown and striped hyenas despite no signs of inbreeding, putatively linked to their similarly slow decline in effective population size over the last ∼2 million years. High levels of genetic diversity and more stable population sizes through time are seen in the spotted hyena and aardwolf. Taken together, our findings highlight how ecological specialization can impact the evolutionary history, demographics, and adaptive genetic changes of an evolutionary lineage.

Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae.

Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes and searching for species-specific structural variants. Among candidate loci associated with phenotypic traits, we observed many related to diet, body condition and reproduction. For example, for the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observed species-specific changes in many pregnancy-related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many changes in genes associated with diet and body condition. All types of genomic variation examined (single nucleotide polymorphisms, gene family expansions, structural variants) contributed substantially to the identification of candidate loci. This argues strongly for consideration of variation other than single nucleotide polymorphisms in comparative genomics studies aiming to identify loci of adaptive significance.

Contrasting levels of hybridization across the two contact zones between two hedgehog species revealed by genome-wide SNP data.

Hybridization and introgression have played important roles in the history of various species, including lineage diversification and the evolution of adaptive traits. Hybridization can accelerate the development of reproductive isolation between diverging species, and thus valuable insight into the evolution of reproductive barrier formation may be gained by studying secondary contact zones. Hedgehogs of the genus Erinaceus, which are insectivores sensitive to changes in climate, are a pioneer model in Pleistocene phylogeography. The present study provides the first genome-wide SNP data regarding the Erinaceus hedgehogs species complex, offering a unique comparison of two secondary contact zones between Erinaceus europaeus and E. roumanicus. Results confirmed diversification of the genus during the Pleistocene period, and detected a new refugial lineage of E. roumanicus outside the Mediterranean basin, most likely in the Ponto-Caspian region. In the Central European zone, the level of hybridization was low, whereas in the Russian-Baltic zone, both species hybridise extensively. Asymmetrical gene flow from E. europaeus to E. roumanicus suggests that reproductive isolation varies according to the direction of the crosses in the hybrid zones. However, no loci with significantly different patterns of introgression were detected. Markedly different pre- and post-zygotic barriers, and thus diverse modes of species boundary maintenance in the two contact zones, likely exist. This pattern is probably a consequence of the different age and thus of the different stage of evolution of reproductive isolating mechanisms in each hybrid zone.

Use of green alternative solvents in dispersive liquid-liquid microextraction: A review.

Dispersive liquid-liquid microextraction is one of the most widely used microextraction techniques currently in the analytical chemistry field, mainly due to its simplicity and rapidity. The operational mode of this approach has been constantly changing since its introduction, adapting to new trends and applications. Most of these changes are related to the nature of the solvent employed for the microextraction. From the classical halogenated solvents (e.g., chloroform or dichloromethane), different alternatives have been proposed in order to obtain safer and non-pollutants microextraction applications. In this sense, low-density solvents, such as alkanols, switchable hydrophobicity solvents, and ionic liquids were the first and most popular replacements for halogenated solvents, which provided similar or better results than these classical dispersive liquid-liquid microextraction solvents. However, despite the good performances obtained with low-density solvents and ionic liquids, researchers have continued investigating in order to obtain even greener solvents for dispersive liquid-liquid microextraction. For that reason, in this review, the evolution over the last five years of the three types of solvents already mentioned and two of the most promising solvent alternatives (i.e., deep eutectic solvents and supramolecular solvents), have been studied in detail with the purpose of discussing which one provides the greenest alternative.

The developmental transcriptome for Lytechinus variegatus exhibits temporally punctuated gene expression changes.

Embryonic development is arguably the most complex process an organism undergoes during its lifetime, and understanding this complexity is best approached with a systems-level perspective. The sea urchin has become a highly valuable model organism for understanding developmental specification, morphogenesis, and evolution. As a non-chordate deuterostome, the sea urchin occupies an important evolutionary niche between protostomes and vertebrates. Lytechinus variegatus (Lv) is an Atlantic species that has been well studied, and which has provided important insights into signal transduction, patterning, and morphogenetic changes during embryonic and larval development. The Pacific species, Strongylocentrotus purpuratus (Sp), is another well-studied sea urchin, particularly for gene regulatory networks (GRNs) and cis-regulatory analyses. A well-annotated genome and transcriptome for Sp are available, but similar resources have not been developed for Lv. Here, we provide an analysis of the Lv transcriptome at 11 timepoints during embryonic and larval development. Temporal analysis suggests that the gene regulatory networks that underlie specification are well-conserved among sea urchin species. We show that the major transitions in variation of embryonic transcription divide the developmental time series into four distinct, temporally sequential phases. Our work shows that sea urchin development occurs via sequential intervals of relatively stable gene expression states that are punctuated by abrupt transitions.

When a viral eruption hides another one: intrafamilial outbreak of parvovirus B19 and measles virus co-infections: case report.

BACKGROUND: Despite high overall population vaccine coverage, identified clusters of persons refraining from vaccination interfere with pursued measles elimination. Clinical diagnosis of measles is often obvious due to its typical rash. Yet, febrile rashes may occur during many viral infections. Misdiagnosis of a specific primary viral infection may have severe consequences, particularly in immunocompromised subjects or pregnant women. To our knowledge, this case presentation is the first description of a measles and parvovirus B19 coinfection outbreak. Analysis of this outbreak underlines rash diagnosis difficulties and potential serology interpretation pitfalls. This case report is helpful for the clinicians in the context of measles re-emergence and proposes several methods to improve the diagnosis approach. CASE PRESENTATION: We investigated an outbreak of rash in 6 out of 8 Traveler family members presenting to Rennes University Hospital (West of France). Anti-B19V and measles IgM/IgG antibodies were measured and detection of Parvovirus B19 and measles virus genomes were done on blood and/or respiratory samples. Virological investigations finally documented 6 cases of parvovirus B19 infections, including 4 associated with measles. Interestingly, in the four coinfection cases, the rash was typical of B19V primary infection for the two children but typical of measles for the two adults. Clinical diagnosis of rash may be misleading and thorough virological investigations may be required to avoid misdiagnosis. CONCLUSIONS: This investigation first reports an intra-familial outbreak of MeV/B19V coinfections highlighting the high transmissibility of both viruses and the diagnostic challenges of dual rash-associated infections. This report also underlines the potential deleterious consequences of failure to identify measles cases, especially in a community with low vaccination coverage.

Targeted vaccination campaigns of teenagers after two clusters of B invasive meningococcal disease in Brittany, France, 2017.

BACKGROUND: In December 2016, three cases of serogroup B invasive meningococcal disease, including two children from the same middle school (11 to 15 years old pupils), occurred in the department (administrative district) Côtes-d'Armor (Brittany, France). They were infected by a rare strain (B:P1.7-2,4:F5-9:cc162), covered by the 4CMenB vaccine (Bexsero®). Four months later, two cases due to the same strain occurred in a high school in the same area (15 to 19 years old students). In accordance with French recommendations, vaccination was proposed to students of both schools and to all individuals aged 11-19 years living or studying in the hyperendemic area. We describe these vaccination campaigns, from the alert to the impact evaluation. METHODS: The target population included 8884 people: 579 in the middle school, 2007 in the high school and 6298 in the community. In both schools, vaccination sessions were organized directly on site. In the community, teenagers were vaccinated by general practitioners. The vaccination campaign took place from May to October 2017. An active pharmacovigilance follow-up was set up to document adverse effects of the vaccine. RESULTS: Considering the whole target population, the vaccination coverage was estimated at 43% for 1 dose and 34% for 2 doses. Higher vaccination coverage was observed in the schools (79% in the middle school and 42% in the high school for 2 doses) than in the community (27% for 2 doses). The reported adverse effects were consistent with the safety profile of the vaccine and no severe adverse effect was reported. CONCLUSIONS: This vaccination campaign was the third one implemented with Bexsero® in France and constitutes a reproducible approach for future targeted vaccination campaigns. No additional cases of the same strain have occurred since the end of the campaigns in the area.

Use of Nanomaterial-Based (Micro)Extraction Techniques for the Determination of Cosmetic-Related Compounds.

The high consumer demand for cosmetic products has caused the authorities and the industry to require rigorous analytical controls to assure their safety and efficacy. Thus, the determination of prohibited compounds that could be present at trace level due to unintended causes is increasingly important. Furthermore, some cosmetic ingredients can be percutaneously absorbed, further metabolized and eventually excreted or bioaccumulated. Either the parent compound and/or their metabolites can cause adverse health effects even at trace level. Moreover, due to the increasing use of cosmetics, some of their ingredients have reached the environment, where they are accumulated causing harmful effects in the flora and fauna at trace levels. To this regard, the development of sensitive analytical methods to determine these cosmetic-related compounds either for cosmetic control, for percutaneous absorption studies or for environmental surveillance monitoring is of high interest. In this sense, (micro)extraction techniques based on nanomaterials as extraction phase have attracted attention during the last years, since they allow to reach the desired selectivity. The aim of this review is to provide a compilation of those nanomaterial-based (micro)extraction techniques for the determination of cosmetic-related compounds in cosmetic, biological and/or environmental samples spanning from the first attempt in 2010 to the present.

An outbreak of leptospirosis among kayakers in Brittany, North-West France, 2016.

In September 2016, a cluster of seven kayakers with clinical symptoms of leptospirosis with onset since July 2016 was reported to French health authorities. Human and animal investigations were undertaken to describe the outbreak, identify the likely place and source of infection and implement necessary control measures. We identified 103 patients with clinical symptoms of leptospirosis between 1 June and 31 October 2016 who lived in the Ille-et-Vilaine district in Brittany. Of these, 14 (including the original seven) reported contacts with the river Vilaine during the incubation period and were defined as outbreak cases: eight were confirmed by serology tests or PCR and six were probable without a laboratory confirmation for leptospirosis. All 14 cases were kayakers. Three distinct contamination sites were identified on a 30 km stretch of the river Vilaine. Nine cases reported having skin wounds while kayaking. None were vaccinated against leptospirosis. The outbreak was attributed to Leptospira kirschneri serogroup Grippotyphosa. Animal investigations did not allow identifying the possible reservoir. Leptospirosis outbreaks associated with freshwater sports are rare in temperate climates. The prevention of such outbreaks requires control of potential animal reservoirs in zones such as the Vilaine valley and that kayakers adopt the recommended individual prevention measures.

LTR retroelements are intrinsic components of transcriptional networks in frogs.

BACKGROUND: LTR retroelements (LTR REs) constitute a major group of transposable elements widely distributed in eukaryotic genomes. Through their own mechanism of retrotranscription LTR REs enrich the genomic landscape by providing genetic variability, thus contributing to genome structure and organization. Nonetheless, transcriptomic activity of LTR REs still remains an obscure domain within cell, developmental, and organism biology. RESULTS: Here we present a first comparative analysis of LTR REs for anuran amphibians based on a full depth coverage transcriptome of the European pool frog, Pelophylax lessonae, the genome of the African clawed frog, Silurana tropicalis (release v7.1), and additional transcriptomes of S. tropicalis and Cyclorana alboguttata. We identified over 1000 copies of LTR REs from all four families (Bel/Pao, Ty1/Copia, Ty3/Gypsy, Retroviridae) in the genome of S. tropicalis and discovered transcripts of several of these elements in all RNA-seq datasets analyzed. Elements of the Ty3/Gypsy family were most active, especially Amn-san elements, which accounted for approximately 0.27% of the genome in Silurana. Some elements exhibited tissue specific expression patterns, for example Hydra1.1 and MuERV-like elements in Pelophylax. In S. tropicalis considerable transcription of LTR REs was observed during embryogenesis as soon as the embryonic genome became activated, i.e. at midblastula transition. In the course of embryonic development the spectrum of transcribed LTR REs changed; during gastrulation and neurulation MuERV-like and SnRV like retroviruses were abundantly transcribed while during organogenesis transcripts of the XEN1 retroviruses became much more active. CONCLUSIONS: The differential expression of LTR REs during embryogenesis in concert with their tissue-specificity and the protein domains they encode are evidence for the functional roles these elements play as integrative parts of complex regulatory networks. Our results support the meanwhile widely accepted concept that retroelements are not simple "junk DNA" or "harmful genomic parasites" but essential components of the transcriptomic machinery in vertebrates.

A new method for morphometric analysis of opal phytoliths from plants.

Micro-morphometry has substantially gained ground in the field of phytolith analysis, but the comparability of results is limited due to the use of different methods. This paper presents a new, user-friendly method based on open-source software (FIJI) that is proposed as a step towards the introduction of a standard method. After obtaining a mask of a phytolith by making a digital drawing, 27 commonly used variables of size and shape are measured automatically. This method is not only useful for phytolith analysis, but may also be used for other fields of morphometric research. Users can furthermore customize the software tool when additional variables are required.

Timely Monitoring of SARS-CoV-2 RNA Fragments in Wastewater Shows the Emergence of JN.1 (BA.2.86.1.1, Clade 23I) in Berlin, Germany.

The importance of COVID-19 surveillance from wastewater continues to grow since case-based surveillance in the general population has been scaled back world-wide. In Berlin, Germany, quantitative and genomic wastewater monitoring for SARS-CoV-2 is performed in three wastewater treatment plants (WWTP) covering 84% of the population since December 2021. The SARS-CoV-2 Omicron sublineage JN.1 (B.2.86.1.1), was first identified from wastewater on 22 October 2023 and rapidly became the dominant sublineage. This change was accompanied by a parallel and still ongoing increase in the notification-based 7-day-hospitalization incidence of COVID-19 and COVID-19 ICU utilization, indicating increasing COVID-19 activity in the (hospital-prone) population and a higher strain on the healthcare system. In retrospect, unique mutations of JN.1 could be identified in wastewater as early as September 2023 but were of unknown relevance at the time. The timely detection of new sublineages in wastewater therefore depends on the availability of new sequences from GISAID and updates to Pango lineage definitions and Nextclade. We show that genomic wastewater surveillance provides timely public health evidence on a regional level, complementing the existing indicators.

Colonial-driven extinction of the blue antelope despite genomic adaptation to low population size.

Low genomic diversity is generally indicative of small population size and is considered detrimental by decreasing long-term adaptability.1,2,3,4,5,6 Moreover, small population size may promote gene flow with congeners and outbreeding depression.7,8,9,10,11,12,13 Here, we examine the connection between habitat availability, effective population size (Ne), and extinction by generating a 40× nuclear genome from the extinct blue antelope (Hippotragus leucophaeus). Historically endemic to the relatively small Cape Floristic Region in southernmost Africa,14,15 populations were thought to have expanded and contracted across glacial-interglacial cycles, tracking suitable habitat.16,17,18 However, we found long-term low Ne, unaffected by glacial cycles, suggesting persistence with low genomic diversity for many millennia prior to extinction in ∼AD 1800. A lack of inbreeding, alongside high levels of genetic purging, suggests adaptation to this long-term low Ne and that human impacts during the colonial era (e.g., hunting and landscape transformation), rather than longer-term ecological processes, were central to its extinction. Phylogenomic analyses uncovered gene flow between roan (H. equinus) and blue antelope, as well as between roan and sable antelope (H. niger), approximately at the time of divergence of blue and sable antelope (∼1.9 Ma). Finally, we identified the LYST and ASIP genes as candidates for the eponymous bluish pelt color of the blue antelope. Our results revise numerous aspects of our understanding of the interplay between genomic diversity and evolutionary history and provide the resources for uncovering the genetic basis of this extinct species' unique traits.

A high-throughput magnetic-based pipette tip microextraction as an alternative to conventional pipette tip strategies: Determination of testosterone in human saliva as a proof-of-concept.

In this work, a lab-made and affordable high-throughput pipette tip microextraction strategy is presented. In this approach, a magnetic sorbent is quickly dispersed in the sample by means of a disperser solvent and the resulting dispersion is immediately aspirated into a pipette tip containing a small neodymium magnet inside, which entraps the magnetic sorbent containing the analytes. The sample is then discarded, and the subsequent cleaning and desorption steps are conducted by aspirating/dispensing the suitable solvents. This methodology provides satisfactory results when compared with previous pipette tip extraction strategies (i.e., pipette-tip solid-phase extraction and dispersive pipette extraction). Furthermore, it requires a minimum number of aspirating/dispensing cycles, thus benefiting the ergonomics for the operator, and it is not commercially dependent. This new approach has been tested by measuring testosterone levels in saliva of volunteers as a proof-of-concept. In this regard, a magnetic composite made of CoFe2O4 magnetic nanoparticles embedded in octadecyl bonded silica microparticles was employed as sorbent material. Testosterone was quantified by liquid chromatography coupled to tandem mass spectrometry. Under the optimized conditions, low limits of detection and quantification (7.5 ng L-1 and 24.8 ng L-1, respectively), good repeatability (RSD <9%) and relative recoveries between 82 and 106% were obtained with just one adsorption and two desorption cycles, which requires few seconds per sample. In order to increase even more the sample throughput, a multichannel pipette was also evaluated.

Low toxicity deep eutectic solvent-based ferrofluid for the determination of UV filters in environmental waters by stir bar dispersive liquid microextraction.

In this work, a low toxicity deep eutectic solvent-based ferrofluid is presented for the first time as magnetic fluid to be used as an efficient solvent in liquid-based microextraction techniques. This ferrofluid is made of a hydrophobic deep eutectic solvent, composed by menthol and thymol in a 1:5 molar ratio as carrier solvent, and oleic acid-coated cobalt ferrite (CoFe2O4@oleic acid) magnetic nanoparticles. This material was characterized via magnetism measurement, scanning electron microscopy, infrared spectroscopy and density measurement. The determination of UV filters in environmental water samples was selected as model analytical application to test the extraction performance of this new ferrofluid by employing stir bar dispersive liquid microextraction, prior to liquid chromatography-tandem mass spectrometry analysis. The response surface methodology was used as a multivariate optimization method for extraction step. Under the optimized conditions, good analytical features were obtained, such as low limits of detection between 7 and 83 ng L-1, good repeatability (relative standard deviations, RSD (%) below 15%), enrichment factors between 46 and 101 and relative recoveries between 80 and 117%, proving the good extraction capability of this ferrofluid. Finally, the method was successfully applied to three environmental waters (beach and river waters), finding trace amounts of the target UV filters. The presented low toxicity deep eutectic solvent-based ferrofluid results to be a good alternative to conventional solvents used in liquid-phase microextraction techniques.