Massive and rapid predominantly volcanic CO2 emission during the end-Permian mass extinction.

The end-Permian mass extinction event (∼252 Mya) is associated with one of the largest global carbon cycle perturbations in the Phanerozoic and is thought to be triggered by the Siberian Traps volcanism. Sizable carbon isotope excursions (CIEs) have been found at numerous sites around the world, suggesting massive quantities of 13C-depleted CO2 input into the ocean and atmosphere system. The exact magnitude and cause of the CIEs, the pace of CO2 emission, and the total quantity of CO2, however, remain poorly known. Here, we quantify the CO2 emission in an Earth system model based on new compound-specific carbon isotope records from the Finnmark Platform and an astronomically tuned age model. By quantitatively comparing the modeled surface ocean pH and boron isotope pH proxy, a massive (∼36,000 Gt C) and rapid emission (∼5 Gt C yr-1) of largely volcanic CO2 source (∼-15%) is necessary to drive the observed pattern of CIE, the abrupt decline in surface ocean pH, and the extreme global temperature increase. This suggests that the massive amount of greenhouse gases may have pushed the Earth system toward a critical tipping point, beyond which extreme changes in ocean pH and temperature led to irreversible mass extinction. The comparatively amplified CIE observed in higher plant leaf waxes suggests that the surface waters of the Finnmark Platform were likely out of equilibrium with the initial massive centennial-scale release of carbon from the massive Siberian Traps volcanism, supporting the rapidity of carbon injection. Our modeling work reveals that carbon emission pulses are accompanied by organic carbon burial, facilitated by widespread ocean anoxia.

Steering opinion dynamics through control of social networks.

In this paper, we propose a novel control approach for opinion dynamics on evolving networks. The controls modify the strength of connections in the network, rather than influencing opinions directly, with the overall goal of steering the population toward a target opinion. This requires that the social network remains sufficiently connected, the population does not break into separate opinion clusters, and that the target opinion remains accessible. We present several approaches to address these challenges, considering questions of controllability, instantaneous control, and optimal control. Each of these approaches provides a different view on the complex relationship between opinion and network dynamics and raises interesting questions for future research.

Dietary Modulation of the Human Gut Microbiota and Metabolome with Flaxseed Preparations.

Flaxseeds are typically consumed either as whole flaxseed, ground flaxseed, flaxseed oil, partially defatted flaxseed meal, or as a milk alternative. They are considered a rich source of vitamins, minerals, proteins and peptides, lipids, carbohydrates, lignans, and dietary fiber, which have shown hypolipidemic, antiatherogenic, anticholesterolemic, and anti-inflammatory property activity. Here, an in vitro batch culture model was used to investigate the influence of whole milled flaxseed and partially defatted milled flaxseed press cake on the gut microbiota and the liberation of flaxseed bioactives. Microbial communities were profiled using 16S rRNA gene-based high-throughput sequencing with targeted mass spectrometry measuring lignan, cyclolinopeptide, and bile acid content and HPLC for short-chain fatty acid profiles. Flaxseed supplementation decreased gut microbiota richness with Firmicutes, Proteobacteria, and Bacteroidetes becoming the predominant phyla. Secoisolariciresinol, enterodiol, and enterolactone were rapidly produced with acetic acid, butyric acid, and propionic acid being the predominant acids after 24 h of fermentation. The flaxseed press cake and whole flaxseed were equivalent in microbiota changes and functionality. However, press cake may be superior as a functional additive in a variety of foods in terms of consumer acceptance as it would be more resistant to oxidative changes.

Virulence Factors of Enteric Pathogenic Escherichia coli: A Review.

Escherichia coli are remarkably versatile microorganisms and important members of the normal intestinal microbiota of humans and animals. This harmless commensal organism can acquire a mixture of comprehensive mobile genetic elements that contain genes encoding virulence factors, becoming an emerging human pathogen capable of causing a broad spectrum of intestinal and extraintestinal diseases. Nine definite enteric E. coli pathotypes have been well characterized, causing diseases ranging from various gastrointestinal disorders to urinary tract infections. These pathotypes employ many virulence factors and effectors subverting the functions of host cells to mediate their virulence and pathogenesis. This review summarizes new developments in our understanding of diverse virulence factors associated with encoding genes used by different pathotypes of enteric pathogenic E. coli to cause intestinal and extraintestinal diseases in humans.

Enzymatic Modification of Native Chitin and Conversion to Specialty Chemical Products.

: Chitin is one of the most abundant biomolecules on earth, occurring in crustacean shells and cell walls of fungi. While the polysaccharide is threatening to pollute coastal ecosystems in the form of accumulating shell-waste, it has the potential to be converted into highly profitable derivatives with applications in medicine, biotechnology, and wastewater treatment, among others. Traditionally this is still mostly done by the employment of aggressive chemicals, yielding low quality while producing toxic by-products. In the last decades, the enzymatic conversion of chitin has been on the rise, albeit still not on the same level of cost-effectiveness compared to the traditional methods due to its multi-step character. Another severe drawback of the biotechnological approach is the highly ordered structure of chitin, which renders it nigh impossible for most glycosidic hydrolases to act upon. So far, only the Auxiliary Activity 10 family (AA10), including lytic polysaccharide monooxygenases (LPMOs), is known to hydrolyse native recalcitrant chitin, which spares the expensive first step of chemical or mechanical pre-treatment to enlarge the substrate surface. The main advantages of enzymatic conversion of chitin over conventional chemical methods are the biocompability and, more strikingly, the higher product specificity, product quality, and yield of the process. Products with a higher Mw due to no unspecific depolymerisation besides an exactly defined degree and pattern of acetylation can be yielded. This provides a new toolset of thousands of new chitin and chitosan derivatives, as the physio-chemical properties can be modified according to the desired application. This review aims to provide an overview of the biotechnological tools currently at hand, as well as challenges and crucial steps to achieve the long-term goal of enzymatic conversion of native chitin into specialty chemical products.

Fission of Polyanionic Metal Clusters.

Size-selected dianionic lead clusters Pb_{n}^{2-}, n=34-56, are stored in a Penning trap and studied with respect to their decay products upon photoexcitation. Contrary to the decay of other dianionic metal clusters, these lead clusters show a variety of decay channels. The mass spectra of the fragments are compared to the corresponding spectra of the monoanionic precursors. This comparison leads to the conclusion that, in the cluster size region below about n=48, the fission reaction Pb_{n}^{2-}→Pb_{n-10}^{-}+Pb_{10}^{-} is the major decay process. Its disappearance at larger cluster sizes may be an indication of a nonmetal to metal transition. Recently, the pair of Pb_{10}^{-} and Pb_{n-10}^{-} were observed as pronounced fragments in electron-attachment studies [S. König et al., Int. J. Mass Spectrom. 421, 129 (2017)IMSPF81387-380610.1016/j.ijms.2017.06.009]. The present findings suggest that this combination is the fingerprint of the decay of doubly charged lead clusters. With this assumption, the dianion clusters have been traced down to Pb_{21}^{2-}, whereas the smallest size for the direct observation was as high as n=28.

Aberrant Classopollis pollen reveals evidence for unreduced (2n) pollen in the conifer family Cheirolepidiaceae during the Triassic-Jurassic transition.

Polyploidy (or whole-genome doubling) is a key mechanism for plant speciation leading to new evolutionary lineages. Several lines of evidence show that most species among flowering plants had polyploidy ancestry, but it is virtually unknown for conifers. Here, we study variability in pollen tetrad morphology and the size of the conifer pollen type Classopollis extracted from sediments of the Triassic-Jurassic transition, 200 Ma. Classopollis producing Cheirolepidiaceae were one of the most dominant and diverse groups of conifers during the Mesozoic. We show that aberrant pollen Classopollis tetrads, triads and dyads, and the large variation in pollen size indicates the presence of unreduced (2n) pollen, which is one of the main mechanisms in modern polyploid formation. Polyploid speciation may explain the high variability of growth forms and adaptation of these conifers to different environments and their resistance to extreme growth conditions. We suggest that polyploidy may have also reduced the extinction risk of these conifers during the End-Triassic biotic crisis.

Rectification properties of conically shaped nanopores: consequences of miniaturization.

Nanopores attracted a great deal of scientific interest as templates for biological sensors as well as model systems to understand transport phenomena at the nanoscale. The experimental and theoretical analysis of nanopores has been so far focused on understanding the effect of the pore opening diameter on ionic transport. In this article we present systematic studies on the dependence of ion transport properties on the pore length. Particular attention was given to the effect of ion current rectification exhibited in conically shaped nanopores with homogeneous surface charges. We found that reducing the length of conically shaped nanopores significantly lowered their ability to rectify ion current. However, rectification properties of short pores can be enhanced by tailoring the surface charge and the shape of the narrow opening. Furthermore we analyzed the relationship of the rectification behavior and ion selectivity for different pore lengths. All simulations were performed using MsSimPore, a software package for solving the Poisson-Nernst-Planck (PNP) equations. It is based on a novel finite element solver and allows for simulations up to surface charge densities of -2 e per nm(2). MsSimPore is based on 1D reduction of the PNP model, but allows for a direct treatment of the pore with bulk electrolyte reservoirs, a feature which was previously used in higher dimensional models only. MsSimPore includes these reservoirs in the calculations, a property especially important for short pores, where the ionic concentrations and the electric potential vary strongly inside the pore as well as in the regions next to the pore entrance.

An explanation for conflicting records of Triassic-Jurassic plant diversity.

Macrofossils (mostly leaves) and sporomorphs (pollen and spores) preserve conflicting records of plant biodiversity during the end-Permian (P-Tr), Triassic-Jurassic (Tr-J), and end-Cretaceous (K-T) mass extinctions. Estimates of diversity loss based on macrofossils are typically much higher than estimates of diversity loss based on sporomorphs. Macrofossils from the Tr-J of East Greenland indicate that standing species richness declined by as much as 85% in the Late Triassic, whereas sporomorph records from the same region, and from elsewhere in Europe, reveal little evidence of such catastrophic diversity loss. To understand this major discrepancy, we have used a new high-resolution dataset of sporomorph assemblages from Astartekløft, East Greenland, to directly compare the macrofossil and sporomorph records of Tr-J plant biodiversity. Our results show that sporomorph assemblages from the Tr-J boundary interval are 10-12% less taxonomically diverse than sporomorph assemblages from the Late Triassic, and that vegetation composition changed rapidly in the boundary interval as a result of emigration and/or extirpation of taxa rather than immigration and/or origination of taxa. An analysis of the representation of different plant groups in the macrofossil and sporomorph records at Astartekløft reveals that reproductively specialized plants, including cycads, bennettites and the seed-fern Lepidopteris are almost absent from the sporomorph record. These results provide a means of reconciling the macrofossil and sporomorph records of Tr-J vegetation change, and may help to understand vegetation change during the P-Tr and K-T mass extinctions and around the Paleocene-Eocene Thermal Maximum.

Revisiting the supraforaminal horizontal oblique osteotomy of the mandible.

PURPOSE: Today, the most common orthognathic procedure for correction of mandibular deformities is the bilateral sagittal split osteotomy, also called sagittal ramus osteotomy. Permanent injury to the mandibular nerve (V3) is one of the main complications, with a reported incidence between 5% and 30%. Orthognathic surgery using sagittal ramus osteotomy of the mandible as the procedure of choice should be re-evaluated because of the complexity and the relatively high risk of damage to the inferior alveolar nerve. Surgical techniques that allow for accurate condylar positioning with a lower risk of inferior alveolar nerve injury should be considered. The aim of this study is to present a retrospective case series using the previously described horizontal osteotomy of the mandibular rami along with modern-day technical advances that make this procedure safe, reliable, and reproducible. MATERIALS AND METHODS: We performed a modified approach to the supraforaminal horizontal oblique osteotomy of the mandible with a condylar positioning device, endoscopy, and a surgical navigation system. This technique was performed in 17 consecutive patients. Postoperatively, we measured the amount of surgical movement of the mandible, monitored the mandibular nerve, and evaluated bone healing during removal of the osteosynthesis plates. RESULTS: In all 17 treated patients there was uneventful wound healing, and no patient had permanent nerve alteration. The mean movement of the mandible was 7.48 mm (SD, 2.1 mm), with a range from 3.0 to 10.5 mm. The mean follow-up was 19 months. The main purpose of the surgical navigation was the translation of the planned osteotomy line from the computed tomography scan to the surgical site during the operation. This was performed to prevent a large gap between the bone segments at the osteotomy site. CONCLUSION: The supraforaminal approach with a condylar positioning device appears to be an appropriate way to prevent injury to the inferior alveolar nerve during orthognathic surgery of the mandible while maintaining centric positioning of the condyle and obtaining good bony union.

Phylogenetic analysis and antibiotic resistance of Shigella sonnei isolates.

Shigellosis is one of the most important gastric infections caused by different species of Shigella, and has been regarded as a serious threat to public health. Lineage/sublineage profile of Shigella sonnei is strongly associated with the antibiotic resistance and population structure of this pathogen. In this study, we determined the phylogeny and antibiotic resistance profiles of S. sonnei strains, isolated from 1246 stool and 580 food samples, using multiplex PCR-HRMA genotyping and Kirby-Bauer disk diffusion methods, respectively. A total of 64 S. sonnei strains were isolated (13 food and 51 clinical isolates). Multiplex PCR-HMR assay was able to differentiate the lineages II and III, and sublineages IIIb and IIIc strains successfully considering the definite melting curves and temperatures. Lineage I and sublineage IIIa strain were not isolated in this study. We also demonstrated that most of the S. sonnei strains isolated from both food and clinical samples clustered within the lineage III and sublineage IIIc. Resistance against trimethoprim-sulfamethoxazole, tetracycline, chloramphenicol, and streptomycin antibiotics were the most prevalent phenotypes among the S. sonnei lineage III and sublineage IIIc strains.

Fermentative Liberation of Ellagic Acid from Walnut Press Cake Ellagitannins.

Oil is extracted from walnut leaves behind large quantities of defatted press cake that is still rich in valuable nutrients. Aspergillus oryzae and Rhizopus oligosporus, two molds traditionally used in Asia, have the necessary enzymes to use the nutrients in the walnut press cake. Walnuts and the press cake contain ellagitannins, known as precursors for ellagic acid and urolithins. In this study, experiments to optimize the solid-state fermentation of walnut press cake were performed in order to liberate ellagic acid from ellagitannins. Extracts of fermented products were then analyzed with an HPLC-DAD to measure the liberation of ellagic acid from ellagitannins. Good growth of R. oligosporus and A. oryzae mycelia on the walnut press cake was observed. A single mold culture was subjected to a hydration of 0.8 mL/g, an addition of 37.5 mmol/kg acetic acid (AA) and 1% NaCl, and an incubation temperature of 25 °C; these were observed to be good conditions for solid-state fermentation for walnut press cake. The highest ellagic acid concentration was obtained at 48 h. At 72 h, degradation dominated the liberation of ellagic acid.

The impact of Miocene atmospheric carbon dioxide fluctuations on climate and the evolution of terrestrial ecosystems.

The Miocene is characterized by a series of key climatic events that led to the founding of the late Cenozoic icehouse mode and the dawn of modern biota. The processes that caused these developments, and particularly the role of atmospheric CO2 as a forcing factor, are poorly understood. Here we present a CO2 record based on stomatal frequency data from multiple tree species. Our data show striking CO2 fluctuations of approximately 600-300 parts per million by volume (ppmv). Periods of low CO2 are contemporaneous with major glaciations, whereas elevated CO2 of 500 ppmv coincides with the climatic optimum in the Miocene. Our data point to a long-term coupling between atmospheric CO2 and climate. Major changes in Miocene terrestrial ecosystems, such as the expansion of grasslands and radiations among terrestrial herbivores such as horses, can be linked to these marked fluctuations in CO2.

A role for atmospheric CO2 in preindustrial climate forcing.

Complementary to measurements in Antarctic ice cores, stomatal frequency analysis of leaves of land plants preserved in peat and lake deposits can provide a proxy record of preindustrial atmospheric CO(2) concentration. CO(2) trends based on leaf remains of Quercus robur (English oak) from the Netherlands support the presence of significant CO(2) variability during the first half of the last millennium. The amplitude of the reconstructed multidecadal fluctuations, up to 34 parts per million by volume, considerably exceeds maximum shifts measured in Antarctic ice. Inferred changes in CO(2) radiative forcing are of a magnitude similar to variations ascribed to other mechanisms, particularly solar irradiance and volcanic activity, and may therefore call into question the concept of the Intergovernmental Panel on Climate Change, which assumes an insignificant role of CO(2) as a preindustrial climate-forcing factor. The stomata-based CO(2) trends correlate with coeval sea-surface temperature trends in the North Atlantic Ocean, suggesting the possibility of an oceanic source/sink mechanism for the recorded CO(2) changes.

A new prokaryotic farnesyldiphosphate synthase from the octocoral Eunicea fusca: differential display, inverse PCR, cloning, and characterization.

We recently reported that the biosynthesis of fuscol, a diterpene from the octocoral Eunicea fusca, is inducible by the application of plant signaling factors such as salicylic acid to the coral's algal symbiont. In this study, an mRNA differential display approach has been employed with the dinoflagellate symbiont of this octocoral which has led to the isolation of a farnesyldiphosphate synthase (FPPS) that was transcriptionally activated under conditions that led to an induction of fuscol biosynthesis. Using a degenerate primer based on the aspartate-rich motifs found in prenylsynthases and a cassette ligation strategy, we report the cloning of the complete FPPS associated with the E. fusca dinoflagellate symbiont Symbiodinium sp. The protein exhibited the enzymatic properties associated with FPPS, namely, the synthesis of farnesyl diphosphate from geranyldiphosphate and isopentenyl diphosphate. The amino acid sequence of this FPPS has a high sequence similarity (82%) to known archaeal isoprenyl diphosphate synthases. This is the first description of a prokaryotic FPPS derived from a marine source.

Diversity of the bacterial communities associated with the azooxanthellate deep water octocorals Leptogorgia minimata, Iciligorgia schrammi, and Swiftia exertia.

This study examined the microbiota associated with the marine azooxanthellate octocorals Leptogorgia minimata, Swiftia exertia, and Iciligorgia schrammi collected from moderate depths (45 m). Traditional aerobic plate culture, fluorescence in situ hybridization (FISH), and molecular identification of the 16S rDNA region were used for this purpose. In general, cultures were found to be selective for Gammaproteobacteria, Alphaproteobacteria, and Firmicutes. Interestingly, FISH counts for Firmicutes in the whole coral (holobiont) were near the detection limit of this assay, representing less than 6% of the total detectable microbiota in all counts. Proteobacteria, especially Alpha- and Gammaproteobacteria, made up the majority of the total microbiota in the holobionts. In addition, the absence of zooxanthellae in these three corals was confirmed by the use of polymerase chain reaction (PCR) and dinoflagellate-specific primers, and spectrophotometric chlorophyll pigment measurements. No evidence of zooxanthellae could be found in any of the corals by either of these techniques. This is the first study examining the microbiota marine octocorals, which grow at moderate depth (40 to 100 m) in the absence of direct sunlight.

Isolation of proteolytic bacteria from mealworm (Tenebrio molitor) exoskeletons to produce chitinous material.

The use of insects as a source of protein is becoming an important factor for feeding an increasing population. After protein extraction for food use, the insect exoskeleton may offer the possibility for the production of added value products. Here, the aim was to isolate bacteria from the surface of farmed mealworms (Tenebrio molitor Linnaeus, 1758) for the production of chitinous material from insect exoskeletons using microbial fermentation. Isolates were screened for proteases and acid production that may aid deproteination and demineralisation of insects through fermentation to produce chitin. Selected isolates were used single-step (isolated bacteria only) or two-step fermentations with Lactobacillus plantarum (DSM 20174). Two-step fermentations with isolates from mealworm exoskeletons resulted in a demineralisation of 97.9 and 98.5% from deproteinated mealworm fractions. Attenuated total reflectance-Fourier- transform infrared spectroscopy analysis showed that crude chitin was produced. However, further optimisation is needed before the process can be upscaled. This is, to our knowledge, the first report using microbial fermentation for the extraction of chitin from insects.

Astronomical age constraints and extinction mechanisms of the Late Triassic Carnian crisis.

The geological record contains evidence for numerous pronounced perturbations in the global carbon cycle, some of which are associated with mass extinction. In the Carnian (Late Triassic), evidence from sedimentology and fossil pollen points to a significant change in climate, resulting in biotic turnover, during a time termed the 'Carnian Pluvial Episode' (CPE). Evidence from the marine realm suggests a causal relationship between the CPE, a global 'wet' period, and the injection of light carbon into the atmosphere. Here we provide the first evidence from a terrestrial stratigraphic succession of at least five significant negative C-isotope excursions (CIE)'s through the CPE recorded in both bulk organic carbon and compound specific plant leaf waxes. Furthermore, construction of a floating astronomical timescale for 1.09 Ma of the Late Triassic, based on the recognition of 405 ka eccentricity cycles in elemental abundance and gamma ray (GR) data, allows for the estimation of a duration for the isotope excursion(s). Source mixing calculations reveal that the observed substantial shift(s) in δ13C was most likely caused by a combination of volcanic emissions, subsequent warming and the dissociation of methane clathrates.

The effects of alpha-lactalbumin and glycomacropeptide on the association of CaCo-2 cells by enteropathogenic Escherichia coli, Salmonella typhimurium and Shigella flexneri.

Two milk components, alpha-lactalbumin (alpha-La) and glycomacropeptide (GMP) may inhibit intestinal infection/intoxification. (3)[H] thymidine-labeled enteropathogenic Escherichia coli (EPEC), Salmonella typhimurium (ATCC 6994) or Shigella flexneri (ATCC 9199) were introduced to CaCo-2 cultures and their association with CaCo-2 cells was assessed. Undigested, pepsin-digested and pepsin- and pancreatin-digested alpha-lactalbumin and glycomacropeptide inhibited association. Thus, milk supplemented with alpha-lactalbumin and glycomacropeptide might be effective in inhibiting associations of the pathogens EPEC, Salmonella typhimurium, and Shigella flexneri to intestinal cells.

Effects of bovine alpha-lactalbumin and casein glycomacropeptide-enriched infant formulae on faecal microbiota in healthy term infants.

OBJECTIVE: Certain milk factors may promote the growth of a host-friendly gastrointestinal microbiota, for example, one that is predominated by bifidobacteria, a perceived health-promoting genus. This may explain why breast-fed infants experience fewer intestinal infections than their formula-fed counterparts who are believed to have a more diverse microbiota, which is similar to that of adults. The effects of formulas supplemented with 2 such ingredients from bovine milk, alpha-lactalbumin (alpha-lac) and casein glycomacropeptide (GMP), on gut flora were investigated in this study. PATIENTS AND METHODS: Six-week-old (4-8 wk), healthy term infants were randomised to a standard infant formula or 1 of 2 test formulae enriched in alpha-lac with higher or lower GMP until 6 months. Faecal bacteriology was determined by the culture-independent procedure fluorescence in situ hybridisation. RESULTS: There was a large fluctuation of bacterial counts within groups with no statistically significant differences between groups. Although all groups showed a predominance of bifidobacteria, breast-fed infants had a small temporary increase in counts. Other bacterial levels varied in formula-fed groups, which overall showed an adult-like faecal microflora. CONCLUSIONS: It can be speculated that a prebiotic effect for alpha-lac and GMP is achieved only with low starting populations of beneficial microbiota (eg, infants not initially breast-fed.