Most genetic roots of fungal and animal aging are hundreds of millions of years old according to phylostratigraphy analyses of aging networks.

Few studies have systematically analyzed how old aging is. Gaining a more accurate knowledge about the natural history of aging could however have several payoffs. This knowledge could unveil lineages with dated genetic hardware, possibly maladapted to current environmental challenges, and also uncover "phylogenetic modules of aging," i.e., naturally evolved pathways associated with aging or longevity from a single ancestry, with translational interest for anti-aging therapies. Here, we approximated the natural history of the genetic hardware of aging for five model fungal and animal species. We propose a lower-bound estimate of the phylogenetic age of origination for their protein-encoding gene families and protein-protein interactions. Most aging-associated gene families are hundreds of million years old, older than the other gene families from these genomes. Moreover, we observed a form of punctuated evolution of the aging hardware in all species, as aging-associated families born at specific phylogenetic times accumulate preferentially in genomes. Most protein-protein interactions between aging genes are also old, and old aging-associated proteins showed a reduced potential to contribute to novel interactions associated with aging, suggesting that aging networks are at risk of losing in evolvability over long evolutionary periods. Finally, due to reshuffling events, aging networks presented a very limited phylogenetic structure that challenges the detection of "maladaptive" or "adaptative" phylogenetic modules of aging in present-day genomes.

Climate extremes in Svalbard over the last two millennia are linked to atmospheric blocking.

Arctic precipitation in the form of rain is forecast to become more prevalent in a warmer world but with seasonal and interannual changes modulated by natural modes of variability. Experiencing rapid hydroclimatic changes in the Arctic, Svalbard serves as an ideal study location due to its exposure to oceanic and atmospheric variability in the North Atlantic region. Here we use climate data from paleoproxies, observations, and a climate model to demonstrate that wet and warm extremes in Svalbard over the last two millennia are linked to the presence of atmospheric blocking regimes over Scandinavia and the Ural mountain region. Rainfall episodes lead to the deposition of coarse sediment particles and high levels of calcium in Linnévatnet, a lake in southwest Svalbard, with the coarsest sediments consistently deposited during atmospheric blocking events. A unique annually resolved sediment record from Linnévatnet confirms that this linkage has been persistent over the past 2000 years. Our record also shows that a millennial-scale decline in Svalbard precipitation ended around the middle of the 19th century, followed by several unprecedented extreme events in recent years. As warming continues and sea ice recedes, future Svalbard floods will become more intense during episodes of Scandinavian and Ural blocking.

Duration of rupture of membranes and microbiome transmission to the newborn: A prospective study.

OBJECTIVE: To assess whether labour variables (i.e. individuals characteristics, labour characteristics and medical interventions) impact maternal and newborn microbiomes. DESIGN: Prospective monocentric study. SETTING: Saint-Joseph Hospital tertiary maternity unit, in Paris, France. POPULATION: All consecutive primiparous women with a physiological pregnancy and term labour from 15 April to 1 June 2017. METHODS: 16S ribosomal RNA gene sequencing of the maternal vaginal, newborn skin and newborn oral microbiomes from 58 mother-baby dyads. MAIN OUTCOME MEASURES: Analysis of the effects of 19 labour variables on the composition and diversity of these microbiomes. RESULTS: The 19 labour variables explained a significant part of the variability in the vaginal, newborn oral and skin microbiomes (44%-67%). Strikingly, duration of rupture of membranes was the single factor that explained the greatest variability (adjusted R2: 7.7%-8.4%, p ≤ 0.002) and conditioned, by itself, the compositions of the three microbiomes under study. Long duration of rupture of membranes was specifically associated with a lower relative abundance of the Lactobacillus genus (1.7-fold to 68-fold reduction, p < 0.0001) as well as an increase in microbiome diversity, including genera implicated in nosocomial infections. The effects of duration of rupture of membranes were also present in newborns delivered by non-elective caesarean section. CONCLUSIONS: Maternal and newborn microbiomes were greatly affected by labour variables. Duration of rupture of membranes, even in non-elective caesarean sections, should be considered in epidemiological and microbiological studies, as well as in vaginal seeding practices.

Silver Nanoparticles Anchored on Single-Walled Carbon Nanotubes via a Conjugated Polymer for Enhanced Sensing Applications.

Single-walled carbon nanotubes (SWCNTs) are candidate matrices for loading metal nanoparticles (NPs) for sensor and catalytic applications owing to their high electron conductivity and mechanical strength, larger surface area, excellent chemical stability, and ease of surface modification. The performance of the formed NP/SWCNT composites is dependent on the NP size, the physical and chemical interactions between the components, and the charge transfer capabilities. Anchoring metal complexes onto the surface of SWCNTs through noncovalent interactions is a viable strategy for achieving high-level metal dispersion and high charge transfer capacities between metal NPs and SWCNTs. However, traditional metal complexes have small molecular sizes, and their noncovalent interactions with SWCNTs are limited to provide excellent sensing and catalytic capability with restricted efficiency and durability. Here, we selected poly(9,9-di-n-dodecylfluorenyl-2,7-diyl-alt-2,2'-bipyridine-5,5') (PFBPy) to increase the noncovalent interactions between silver nanoparticles (AgNPs) and SWCNTs. A silver triflate (Ag-OTf) solution was added into a PFBPy-wrapped SWCNT solution to form Ag-PFBPy complexes on the nanotube surface, after which Ag+ was photoreduced to AgNPs to form a Ag-PFBPy/SWCNT composite in the solution. In various feeding molar ratios of Ag-OTf over the BPy unit (0.4-50), the size of the formed AgNPs may be well-controlled at sub-nm levels to provide them with an energy level comparable to that of the SWCNTs. Additionally, the 2,2'-bipyridine (BPy) unit of the polymer provided a coordinating interaction with Ag+ and the formed AgNPs as well. The 5,5'-linage of BPy with the fluorene unit in PFBPy ensured a straight main chain structure to retain strong π-π interactions with nanotubes before and after Ag+ chelation. All of these factors confirmed a tight contact between the formed AgNPs and SWCNTs, promoting the charge transfer between them and enhancing the sensing capabilities with a 5-fold increase in humidity sensing sensitivity.

Network analyses unveil ageing-associated pathways evolutionarily conserved from fungi to animals.

The genetic roots of the diverse paces and shapes of ageing and of the large variations in longevity observed across the tree of life are poorly understood. Indeed, pathways associated with ageing/longevity are incompletely known, both in terms of their constitutive genes/proteins and of their molecular interactions. Moreover, there is limited overlap between the genes constituting these pathways across mammals. Yet, dedicated comparative analyses might still unravel evolutionarily conserved, important pathways associated with longevity or ageing. Here, we used an original strategy with a double evolutionary and systemic focus to analyse protein interactions associated with ageing or longevity during the evolution of five species of Opisthokonta. We ranked these proteins and interactions based on their evolutionary conservation and centrality in past and present protein-protein interaction (PPI) networks, providing a big systemic picture of the evolution of ageing and longevity pathways that identified which pathways emerged in which Opisthokonta lineages, were conserved, and/or central. We confirmed that longevity/ageing-associated proteins (LAPs), be they pro- or anti-longevity, are highly central in extant PPI, consistently with the antagonistic pleiotropy theory of ageing, and identified key antagonistic regulators of ageing/longevity, 52 of which with homologues in humans. While some highly central LAPs were evolutionarily conserved for over a billion years, we report a clear transition in the functionally important components of ageing/longevity within bilaterians. We also predicted 487 novel evolutionarily conserved LAPs in humans, 54% of which are more central than mTOR, and 138 of which are druggable, defining new potential targets for anti-ageing treatments in humans.

Proximate Drivers of Population-Level Lizard Gut Microbial Diversity: Impacts of Diet, Insularity, and Local Environment.

Diet has been suggested to be an important driver of variation in microbiota composition in mammals. However, whether this is a more general phenomenon and how fast changes in gut microbiota occur with changes in diet remains poorly understood. Forty-nine years ago, ten lizards of the species Podarcis siculus were taken from the island of Pod Kopiste and introduced onto the island of Pod Mrcaru (Croatia). The introduced population underwent a significant dietary shift, and their descendants became omnivorous (consuming up to 80% plant material during summer). Variation in their gut microbiota has never been investigated. To elucidate the possible impact on the gut microbiota of this rapid change in diet, we compared the microbiota (V4 region of the 16S rRNA gene) of P. siculus from Pod Mrcaru, Pod Kopiste, and the mainland. In addition, we explored other drivers of variation in gut microbiota including insularity, the population of origin, and the year of sampling. Alpha-diversity analyses showed that the microbial diversity of omnivorous lizards was higher than the microbial diversity of insectivorous lizards. Moreover, omnivorous individuals harbored significantly more Methanobrevibacter. The gut microbial diversity of insectivorous lizards was nonetheless more heterogeneous. Insectivorous lizards on the mainland had different gut microbial communities than their counterparts on the island of Pod Kopiste. Bacillus and Desulfovibrio were more abundant in the gut microbiota from insular lizards compared to mainland lizards. Finally, we showed that the population of origin was also an important driver of the composition of the gut microbiota. The dietary shift that occurred in the introduced population of P. siculus has had a detectable impact on the gut microbiota, but other factors such as insularity and the population of origin also contributed to differences in the gut microbial composition of these lizards, illustrating the multifactorial nature of the drivers of variation in gut microbiota. Overall, our data show that changes in gut microbiota may take place on ecological timescales. Yet, diet is only one of many factors driving variation in gut microbiota across populations.

Applying novel connectivity networks to wood turtle populations to provide comprehensive conservation management strategies for species at risk.

Genetic diversity within and among populations is frequently used in prioritization processes to rank populations based on their vulnerability or distinctiveness, however, connectivity and gene flow are rarely considered within these frameworks. Using a wood turtle (Glyptemys insculpta) population graph, we introduce BRIDES as a new tool to evaluate populations for conservation purpose without focusing solely on individual nodes. BRIDES characterizes different types of shortest paths among the nodes of a subgraph and compares the shortest paths among the same nodes in a complete network. The main objectives of this study were to (1) introduce a BRIDES selection process to assist conservation biologists in the prioritization of populations, and (2) use different centrality indices and node removal statistics to compare BRIDES results and assess gene flow among wood turtle populations. We constructed six population subgraphs and used a stepwise selection algorithm to choose the optimal number of additional nodes, representing different populations, required to maximize network connectivity under different weighting schemes. Our results demonstrate the robustness of the BRIDES selection process for a given scenario, while inconsistencies were observed among node-based metrics. Results showed repeated selection of certain wood turtle populations, which could have not been predicted following only genetic diversity and distinctiveness estimation, node-based metrics and node removal analysis. Contrary to centrality measures focusing on static networks, BRIDES allowed for the analysis of evolving networks. To our knowledge, this study is the first to apply graph theory for turtle conservation genetics. We show that population graphs can reveal complex gene flow dynamics and population resiliency to local extinction. As such, BRIDES offers an interesting complement to node-based metrics and node removal to better understand the global processes at play when addressing population prioritization frameworks.

Nanotube abundance from non-negative matrix factorization of Raman spectra as an example of chemical purity from open source machine learning.

The chemical purity of materials is important for semiconductors, including the carbon nanotube material system, which is emerging in semiconductor applications. One approach to get statistically meaningful abundances and/or concentrations is to measure a large number of small samples. Automated multivariate classification algorithms can be used to draw conclusions from such large data sets. Here, we use spatially-mapped Raman spectra of mixtures of chirality-sorted single walled carbon nanotubes dispersed sparsely on flat silicon/silicon oxide substrates. We use non-negative matrix factorization (NMF) decomposition in scikit-learn, an open-source, python language "machine learning" package, to extract spectral components and derive weighting factors. We extract the abundance of minority species (7,5) nanotubes in mixtures by testing both synthetic data, and real samples prepared by dilution. We show how noise limits the purity level that can be evaluated. We determine real situations where this approach works well, and identify situations where it fails.

Aging at Evolutionary Crossroads: Longitudinal Gene Co-expression Network Analyses of Proximal and Ultimate Causes of Aging in Bats.

How, when, and why do organisms, their tissues, and their cells age remain challenging issues, although researchers have identified multiple mechanistic causes of aging, and three major evolutionary theories have been developed to unravel the ultimate causes of organismal aging. A central hypothesis of these theories is that the strength of natural selection decreases with age. However, empirical evidence on when, why, and how organisms age is phylogenetically limited, especially in natural populations. Here, we developed generic comparisons of gene co-expression networks that quantify and dissect the heterogeneity of gene co-expression in conspecific individuals from different age-classes to provide topological evidence about some mechanical and fundamental causes of organismal aging. We applied this approach to investigate the complexity of some proximal and ultimate causes of aging phenotypes in a natural population of the greater mouse-eared bat Myotis myotis, a remarkably long-lived species given its body size and metabolic rate, with available longitudinal blood transcriptomes. M. myotis gene co-expression networks become increasingly fragmented with age, suggesting an erosion of the strength of natural selection and a general dysregulation of gene co-expression in aging bats. However, selective pressures remain sufficiently strong to allow successive emergence of homogeneous age-specific gene co-expression patterns, for at least 7 years. Thus, older individuals from long-lived species appear to sit at an evolutionary crossroad: as they age, they experience both a decrease in the strength of natural selection and a targeted selection for very specific biological processes, further inviting to refine a central hypothesis in evolutionary aging theories.

Little Ice Age abruptly triggered by intrusion of Atlantic waters into the Nordic Seas.

The Little Ice Age (LIA) was one of the coldest periods of the postglacial period in the Northern Hemisphere. Although there is increasing evidence that this time interval was associated with weakening of the subpolar gyre (SPG), the sequence of events that led to its weakened state has yet to be explained. Here, we show that the LIA was preceded by an exceptional intrusion of warm Atlantic water into the Nordic Seas in the late 1300s. The intrusion was a consequence of persistent atmospheric blocking over the North Atlantic, linked to unusually high solar activity. The warmer water led to the breakup of sea ice and calving of tidewater glaciers; weakening of the blocking anomaly in the late 1300s allowed the large volume of ice that had accumulated to be exported into the North Atlantic. This led to a weakening of the SPG, setting the stage for the subsequent LIA.

Corrigendum: Antifungal Potential of the Skin Microbiota of Hibernating Big Brown Bats (Eptesicus fuscus) Infected With the Causal Agent of White-Nose Syndrome.

[This corrects the article DOI: 10.3389/fmicb.2020.01776.].

Annually resolved Atlantic sea surface temperature variability over the past 2,900 y.

Global warming due to anthropogenic factors can be amplified or dampened by natural climate oscillations, especially those involving sea surface temperatures (SSTs) in the North Atlantic which vary on a multidecadal scale (Atlantic multidecadal variability, AMV). Because the instrumental record of AMV is short, long-term behavior of AMV is unknown, but climatic teleconnections to regions beyond the North Atlantic offer the prospect of reconstructing AMV from high-resolution records elsewhere. Annually resolved titanium from an annually laminated sedimentary record from Ellesmere Island, Canada, shows that the record is strongly influenced by AMV via atmospheric circulation anomalies. Significant correlations between this High-Arctic proxy and other highly resolved Atlantic SST proxies demonstrate that it shares the multidecadal variability seen in the Atlantic. Our record provides a reconstruction of AMV for the past ∼3 millennia at an unprecedented time resolution, indicating North Atlantic SSTs were coldest from ∼1400-1800 CE, while current SSTs are the warmest in the past ∼2,900 y.

Probing the Birth and Ultrafast Dynamics of Hydrated Electrons at the Gold/Liquid Water Interface via an Optoelectronic Approach.

The hydrated electron has fundamental and practical significance in radiation and radical chemistry, catalysis, and radiobiology. While its bulk properties have been extensively studied, its behavior at solid/liquid interfaces is still unclear due to the lack of effective tools to characterize this short-lived species in between two condensed matter layers. In this study, we develop a novel optoelectronic technique for the characterization of the birth and structural evolution of solvated electrons at the metal/liquid interface with a femtosecond time resolution. Using this tool, we record for the first time the transient spectra (in a photon energy range from 0.31 to 1.85 eV) in situ with a time resolution of 50 fs revealing several novel aspects of their properties at the interface. Especially the transient species show state-dependent optical transition behaviors from being isotropic in the hot state to perpendicular to the surface in the trapped and solvated states. The technique will enable a better understanding of hot electron driven reactions at electrochemical interfaces.

Antifungal Potential of the Skin Microbiota of Hibernating Big Brown Bats (Eptesicus fuscus) Infected With the Causal Agent of White-Nose Syndrome.

Little is known about skin microbiota in the context of the disease white-nose syndrome (WNS), caused by the fungus Pseudogymnoascus destructans (Pd), that has caused enormous declines of hibernating North American bats over the past decade. Interestingly, some hibernating species, such as the big brown bat (Eptesicus fuscus), appear resistant to the disease and their skin microbiota could play a role. However, a comprehensive analysis of the skin microbiota of E. fuscus in the context of Pd has not been done. In January 2017, we captured hibernating E. fuscus, sampled their skin microbiota, and inoculated them with Pd or sham inoculum. We allowed the bats to hibernate in the lab under controlled conditions for 11 weeks and then sampled their skin microbiota to test the following hypotheses: (1) Pd infection would not disrupt the skin microbiota of Pd-resistant E. fuscus; and (2) microbial taxa with antifungal properties would be abundant both before and after inoculation with Pd. Using high-throughput 16S rRNA gene sequencing, we discovered that beta diversity of Pd-inoculated bats changed more over time than that of sham-inoculated bats. Still, the most abundant taxa in the community were stable throughout the experiment. Among the most abundant taxa, Pseudomonas and Rhodococcus are known for antifungal potential against Pd and other fungi. Thus, in contrast to hypothesis 1, Pd infection destabilized the skin microbiota but consistent with hypothesis 2, bacteria with known antifungal properties remained abundant and stable on the skin. This study is the first to provide a comprehensive survey of skin microbiota of E. fuscus, suggesting potential associations between the bat skin microbiota and resistance to the Pd infection and WNS. These results set the stage for future studies to characterize microbiota gene expression, better understand mechanisms of resistance to WNS, and help develop conservation strategies.

Enrichment of Semiconducting Single-Walled Carbon Nanotubes with Indigo-Fluorene-Based Copolymers and Their Use in Printed Thin-Film Transistors and Carbon Dioxide Gas Sensors.

High-purity semiconducting single-walled carbon nanotubes (sc-SWCNTs) are promising for portable and high-sensitivity gas sensors because of their excellent physical and electrical properties. Here, we describe the synthesis of a novel indigo-fluorene-based copolymer (PFIDBoc) that has been designed to selectively enrich sc-SWCNTs with excellent purity (>99.9%) yet contain a latent function in the form of a tert-butoxy (t-BOC)-protected amine that can be later revealed and exploited for carbon dioxide (CO2) gas sensing. SWCNTs wrapped with the PFIDBoc polymer can be easily converted via an on-chip thermal process to reveal a vinylogous amide moiety with a secondary amine nitrogen within the indigo building block of the copolymer which is perfectly suited for CO2 recognition. Thin-film transistors and sensors were inkjet-printed onto rigid and flexible substrates, demonstrating the versatility of enriched PFIDBoc-derived sc-SWCNT dispersions. The printed transistors exhibited a mobility up to 9 cm2 V-1 s-1 and on/off current ratios >105. We further demonstrate herein a CO2 sensor for indoor air quality monitoring even in low humidity environments, possessing a linear response with up to ∼5.4% sensitivity and a dynamic range between 400 and 2000 ppm in air with a relative humidity of ∼ 40%.

Polymer Encapsulants for Threshold Voltage Control in Carbon Nanotube Transistors.

Although carbon nanotube transistors present outstanding performances based on key metrics, large-scale uniformity and repeatability required in printable electronics depend greatly on proper control of the electrostatic environment. Through a survey of polymer dielectric encapsulants compatible with printing processes, a simple correlation is found between the measured interfacial charge density and the onset of conduction in a transistor, providing a rational route to control the electrical characteristics of carbon nanotube transistors. Smooth and continuous balancing of the properties between unipolar p-type and n-type transport is achieved using a molar fraction series of poly(styrene-co-2-vinylpyridine) statistical copolymers combined with an electron-donating molecule. We further demonstrate the easy fabrication of a p-n diode which shows a modest rectification of 8:1.

Introducing Trait Networks to Elucidate the Fluidity of Organismal Evolution Using Palaeontological Data.

Explaining the evolution of animals requires ecological, developmental, paleontological, and phylogenetic considerations because organismal traits are affected by complex evolutionary processes. Modeling a plurality of processes, operating at distinct time-scales on potentially interdependent traits, can benefit from approaches that are complementary treatments to phylogenetics. Here, we developed an inclusive network approach, implemented in the command line software ComponentGrapher, and analyzed trait co-occurrence of rhinocerotoid mammals. We identified stable, unstable, and pivotal traits, as well as traits contributing to complexes, that may follow to a common developmental regulation, that point to an early implementation of the postcranial Bauplan among rhinocerotoids. Strikingly, most identified traits are highly dissociable, used repeatedly in distinct combinations and in different taxa, which usually do not form clades. Therefore, the genes encoding these traits are likely recruited into novel gene regulation networks during the course of evolution. Our evo-systemic framework, generalizable to other evolved organizations, supports a pluralistic modeling of organismal evolution, including trees and networks.

Probing Ca2+-induced conformational change of calmodulin with gold nanoparticle-decorated single-walled carbon nanotube field-effect transistors.

Nanomaterials are ideal for electrochemical biosensors, with their nanoscale dimensions enabling the sensitive probing of biomolecular interactions. In this study, we compare field-effect transistors (FET) comprised of unsorted (un-) and semiconducting-enriched (sc-) single-walled carbon nanotubes (SWCNTs). un-SWCNTs have both metallic and semiconducting SWCNTs in the ensemble, while sc-SWCNTs have a >99.9% purity of semiconducting nanotubes. Both SWCNT FET devices were decorated with gold nanoparticles (AuNPs) and were then employed in investigating the Ca2+-induced conformational change of calmodulin (CaM) - a vital process in calcium signal transduction in the human body. Different biosensing behavior was observed from FET characteristics of the two types of SWCNTs, with sc-SWCNT FET devices displaying better sensing performance with a dynamic range from 10-15 M to 10-13 M Ca2+, and a lower limit of detection at 10-15 M Ca2+.

Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution.

BACKGROUND: Haloarchaea, a major group of archaea, are able to metabolize sugars and to live in oxygenated salty environments. Their physiology and lifestyle strongly contrast with that of their archaeal ancestors. Amino acid optimizations, which lowered the isoelectric point of haloarchaeal proteins, and abundant lateral gene transfers from bacteria have been invoked to explain this deep evolutionary transition. We use network analyses to show that the evolution of novel genes exclusive to Haloarchaea also contributed to the evolution of this group. RESULTS: We report the creation of 320 novel composite genes, both early in the evolution of Haloarchaea during haloarchaeal genesis and later in diverged haloarchaeal groups. One hundred and twenty-six of these novel composite genes derived from genetic material from bacterial genomes. These latter genes, largely involved in metabolic functions but also in oxygenic lifestyle, constitute a different gene pool from the laterally acquired bacterial genes formerly identified. These novel composite genes were likely advantageous for their hosts, since they show significant residence times in haloarchaeal genomes-consistent with a long phylogenetic history involving vertical descent and lateral gene transfer-and encode proteins with optimized isoelectric points. CONCLUSIONS: Overall, our work encourages a systematic search for composite genes across all archaeal major groups, in order to better understand the origins of novel prokaryotic genes, and in order to test to what extent archaea might have adjusted their lifestyles by incorporating and recycling laterally acquired bacterial genetic fragments into new archaeal genes.

Paternity Analysis of Wood Turtles (Glyptemys insculpta) Reveals Complex Mating Patterns.

Mating system characteristics are of great importance as they may influence male and female reproductive success and reproductive isolation. The wood turtle (Glyptemys insculpta) is a terrestrial freshwater species listed as endangered by the International Union for Conservation of Nature. Considering its conservation status and the paucity of information currently available on parentage relationship for the species, we performed a microsatellite analysis to study the mating system of wood turtles in the Shawinigan River (Québec). We sampled 38 clutches over 2 years (14 in 2006 and 24 in 2007), for a total of 248 offspring genotyped with 7 microsatellite loci. The reconstructed genotypes of the fathers revealed that reproductive success in the sampled clutches varied greatly between males and are positively correlated with the number of mates and clutches sired. Frequency of multiple paternity was estimated at 37% through a consensus of 3 different estimation methods. Positive correlation was observed between the genetic diversity of clutches and the number of fathers. Repeat paternity, however, was observed in 88% of the clutches by the same female in successive years, which suggests either a frequent use of sperm storage, or remating with the same partner in successive years.