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.

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.

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.

CompositeSearch: A Generalized Network Approach for Composite Gene Families Detection.

Genes evolve by point mutations, but also by shuffling, fusion, and fission of genetic fragments. Therefore, similarity between two sequences can be due to common ancestry producing homology, and/or partial sharing of component fragments. Disentangling these processes is especially challenging in large molecular data sets, because of computational time. In this article, we present CompositeSearch, a memory-efficient, fast, and scalable method to detect composite gene families in large data sets (typically in the range of several million sequences). CompositeSearch generalizes the use of similarity networks to detect composite and component gene families with a greater recall, accuracy, and precision than recent programs (FusedTriplets and MosaicFinder). Moreover, CompositeSearch provides user-friendly quality descriptions regarding the distribution and primary sequence conservation of these gene families allowing critical biological analyses of these data.

Urban point sources of nutrients were the leading cause for the historical spread of hypoxia across European lakes.

Enhanced phosphorus (P) export from land into streams and lakes is a primary factor driving the expansion of deep-water hypoxia in lakes during the Anthropocene. However, the interplay of regional scale environmental stressors and the lack of long-term instrumental data often impede analyses attempting to associate changes in land cover with downstream aquatic responses. Herein, we performed a synthesis of data that link paleolimnological reconstructions of lake bottom-water oxygenation to changes in land cover/use and climate over the past 300 years to evaluate whether the spread of hypoxia in European lakes was primarily associated with enhanced P exports from growing urbanization, intensified agriculture, or climatic change. We showed that hypoxia started spreading in European lakes around CE 1850 and was greatly accelerated after CE 1900. Socioeconomic changes in Europe beginning in CE 1850 resulted in widespread urbanization, as well as a larger and more intensively cultivated surface area. However, our analysis of temporal trends demonstrated that the onset and intensification of lacustrine hypoxia were more strongly related to the growth of urban areas than to changes in agricultural areas and the application of fertilizers. These results suggest that anthropogenically triggered hypoxia in European lakes was primarily caused by enhanced P discharges from urban point sources. To date, there have been no signs of sustained recovery of bottom-water oxygenation in lakes following the enactment of European water legislation in the 1970s to 1980s, and the subsequent decrease in domestic P consumption.

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.

Hydrophobic Water Probed Experimentally at the Gold Electrode/Aqueous Interface.

Quantitative description of reaction mechanisms in aqueous phase electrochemistry requires experimental characterization of local water structure at the electrode/aqueous interface and its evolution with changing potential. Gaining such insight experimentally under electrochemical conditions is a formidable task. The potential-dependent structure of a subpopulation of interfacial water with one OH group pointing towards a gold working electrode is characterized using interface specific vibrational spectroscopy in a thin film electrochemical cell. Such free-OH groups are the molecular level observable of an extended hydrophobic interface. This free-OH interacts only weakly with the Au surface at all potentials, has an orientational distribution that narrows approaching the potential of zero charge, and disappears on oxidation of the gold electrode.

Using hybridization networks to retrace the evolution of Indo-European languages.

BACKGROUND: Curious parallels between the processes of species and language evolution have been observed by many researchers. Retracing the evolution of Indo-European (IE) languages remains one of the most intriguing intellectual challenges in historical linguistics. Most of the IE language studies use the traditional phylogenetic tree model to represent the evolution of natural languages, thus not taking into account reticulate evolutionary events, such as language hybridization and word borrowing which can be associated with species hybridization and horizontal gene transfer, respectively. More recently, implicit evolutionary networks, such as split graphs and minimal lateral networks, have been used to account for reticulate evolution in linguistics. RESULTS: Striking parallels existing between the evolution of species and natural languages allowed us to apply three computational biology methods for reconstruction of phylogenetic networks to model the evolution of IE languages. We show how the transfer of methods between the two disciplines can be achieved, making necessary methodological adaptations. Considering basic vocabulary data from the well-known Dyen's lexical database, which contains word forms in 84 IE languages for the meanings of a 200-meaning Swadesh list, we adapt a recently developed computational biology algorithm for building explicit hybridization networks to study the evolution of IE languages and compare our findings to the results provided by the split graph and galled network methods. CONCLUSION: We conclude that explicit phylogenetic networks can be successfully used to identify donors and recipients of lexical material as well as the degree of influence of each donor language on the corresponding recipient languages. We show that our algorithm is well suited to detect reticulate relationships among languages, and present some historical and linguistic justification for the results obtained. Our findings could be further refined if relevant syntactic, phonological and morphological data could be analyzed along with the available lexical data.

Global spread of hypoxia in freshwater ecosystems during the last three centuries is caused by rising local human pressure.

The spread of hypoxia is a threat to aquatic ecosystem functions and services as well as to biodiversity. However, sparse long-term monitoring of lake ecosystems has prevented reconstruction of global hypoxia dynamics while inhibiting investigations into its causes and assessing the resilience capacity of these systems. This study compiles the onset and duration of hypoxia recorded in sediments of 365 lakes worldwide since AD 1700, showing that lacustrine hypoxia started spreading before AD 1900, 70 years prior to hypoxia in coastal zones. This study also shows that the increase of human activities and nutrient release is leading to hypoxia onset. No correlations were found with changes in precipitation or temperature. There is no evidence for a post-1980s return to well-oxygenated lacustrine conditions in industrialized countries despite the implementation of restoration programs. The apparent establishment of stable hypoxic conditions prior to AD 1900 highlights the challenges of a growing nutrient demand, accompanied by increasing global nutrient emissions of our industrialized societies, and climate change.

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.

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.

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.

Harvesting evolutionary signals in a forest of prokaryotic gene trees.

Phylogenomic studies produce increasingly large phylogenetic forests of trees with patchy taxonomical sampling. Typically, prokaryotic data generate thousands of gene trees of all sizes that are difficult, if not impossible, to root. Their topologies do not match the genealogy of lineages, as they are influenced not only by duplication, losses, and vertical descent but also by lateral gene transfer (LGT) and recombination. Because this complexity in part reflects the diversity of evolutionary processes, the study of phylogenetic forests is thus a great opportunity to improve our understanding of prokaryotic evolution. Here, we show how the rich evolutionary content of such novel phylogenetic objects can be exploited through the development of new approaches designed specifically for extracting the multiple evolutionary signals present in the forest of life, that is, by slicing up trees into remarkable bits and pieces: clans, slices, and clips. We harvested a forest of 6,901 unrooted gene trees comprising up to 100 prokaryotic genomes (41 archaea and 59 bacteria) to search for evolutionary events that a species tree would not account for. We identified 1) trees and partitions of trees that reflected the lifestyle of organisms rather than their taxonomy, 2) candidate lifestyle-specific genetic modules, used by distinct unrelated organisms to adapt to the same environment, 3) gene families, nonrandomly distributed in the functional space, that were frequently exchanged between archaea and bacteria, sometimes without major changes in their sequences. Finally, 4) we reconstructed polarized networks of genetic partnerships between archaea and bacteria to describe some of the rules affecting LGT between these two Domains.

Fano resonances in the midinfrared spectra of single-walled carbon nanotubes.

This work revisits the physics giving rise to the carbon nanotube phonon bands in the midinfrared. Our measurements of doped and undoped samples of single-walled carbon nanotubes in Fourier transform infrared spectroscopy show that the phonon bands exhibit an asymmetric line shape and that their effective cross section is enhanced upon doping. We relate these observations to electron-phonon coupling or, more specifically, to a Fano resonance phenomenon. We note that the dopant-induced intraband (not interband) continuum couples strongly to the phonon modes, and that defects created on the sidewall are scattering centers that increase the spectral amplitude of the resonance.

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.

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.

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.

The performance of the Congruence Among Distance Matrices (CADM) test in phylogenetic analysis.

BACKGROUND: CADM is a statistical test used to estimate the level of Congruence Among Distance Matrices. It has been shown in previous studies to have a correct rate of type I error and good power when applied to dissimilarity matrices and to ultrametric distance matrices. Contrary to most other tests of incongruence used in phylogenetic analysis, the null hypothesis of the CADM test assumes complete incongruence of the phylogenetic trees instead of congruence. In this study, we performed computer simulations to assess the type I error rate and power of the test. It was applied to additive distance matrices representing phylogenies and to genetic distance matrices obtained from nucleotide sequences of different lengths that were simulated on randomly generated trees of varying sizes, and under different evolutionary conditions. RESULTS: Our results showed that the test has an accurate type I error rate and good power. As expected, power increased with the number of objects (i.e., taxa), the number of partially or completely congruent matrices and the level of congruence among distance matrices. CONCLUSIONS: Based on our results, we suggest that CADM is an excellent candidate to test for congruence and, when present, to estimate its level in phylogenomic studies where numerous genes are analysed simultaneously.