Alpha- and Gammaproteobacterial Methanotrophs Codominate the Active Methane-Oxidizing Communities in an Acidic Boreal Peat Bog

The objective of this study was to characterize metabolically active, aerobic methanotrophs in an ombrotrophic peatland in the Marcell Experimental Forest, Minnesota, USA. Methanotrophs were investigated in the field and in laboratory incubations using DNA-stable isotope probing, expression studies on particulate methane monooxygenase (pmoA) genes, and amplicon sequencing of 16S rRNA genes. Potential rates of oxidation ranged from 14-17 μmol CH4 g dry wt soil-1 d-1. Within DNA-SIP incubations, the relative abundance of methanotrophs increased from 4% in situ to 25-36% after 8 -14 days. Phylogenetic analysis of the 13C-enriched DNA fractions revealed the active methanotrophs were dominated by the genera Methylocystis (Type II; Alphaproteobacteria), Methylomonas, and Methylovulum (Type I; Gammaproteobacteria). In field samples, a transcript-to-gene ratio of 1 to 2 was observed for pmoA in surface peat layers which attenuated rapidly with depth, indicating the highest methane consumption was associated with the 0-10 cm depth interval. Metagenomes and sequencing of cDNA pmoA amplicons from field samples confirmed the dominant active methanotrophs were Methylocystis and Methylomonas. Although Type II methanotrophs have long been shown to mediate methane consumption in peatlands, our results indicate members of the genera Methylomonas and Methylovulum (Type I) can significantly contribute to aerobic methane oxidation in these ecosystems

Kinetics and crystallization path of a Fe-based metallic glass alloy

The thermal stability and the quantification of the different transformation processes involved in the overall crystallization of the Fe50Cr15Mo14C15B6 amorphous alloy were investigated by several characterization techniques. Formation of various metastable and stable phases during the devitrification process in the sequence a-Fe, ¿-Cr6Fe18Mo5, M23(C,B)6, M7C3, ¿-Fe3Mo3C and FeMo2B2 (with M = Fe, Cr, Mo), was observed by in-situ synchrotron high energy X-ray diffraction and in-situ transmission electron microscopy. By combining these techniques with differential scanning calorimetry data, the crystallization states and their temperature range of stability under continuous heating were related with the evolution of the crystallized fraction and the phase sequence as a function of temperature, revealing structural and chemical details of the different transformation mechanisms.Postprint (published version

Decomposition of fractional quantum Hall states: New symmetries and approximations

We provide a detailed description of a new symmetry structure of the monomial (Slater) expansion coefficients of bosonic (fermionic) fractional quantum Hall states first obtained in Ref. 1, which we now extend to spin-singlet states. We show that the Haldane-Rezayi spin-singlet state can be obtained without exact diagonalization through a differential equation method that we conjecture to be generic to other FQH model states. The symmetry rules in Ref. 1 as well as the ones we obtain for the spin singlet states allow us to build approximations of FQH states that exhibit increasing overlap with the exact state (as a function of system size). We show that these overlaps reach unity in the thermodynamic limit even though our approximation omits more than half of the Hilbert space. We show that the product rule is valid for any FQH state which can be written as an expectation value of parafermionic operators.Comment: 22 pages, 8 figure

Effect of off-stoichiometric compositions on microstructures and phase transformation behavior in Ni-Cu-Pd-Ti-Zr-Hf high entropy shape memory alloys

High entropy shape memory alloys (HE-SMAs) show reversible martensitic phase transformations at elevated temperatures. HE-SMAs were derived from binary NiTi, to which the elements Cu, Pd, Zr and Hf are added. They represent ordered complex solid solutions. Their high temperature phase is of B2 type, where the added elements occupy sites in the Ni-(Cu, Pd) and Ti-sub-lattices (Zr, Hf). In the present study, advanced microstructural and thermal characterization methods were used to study the effects of the additional alloy elements on microstructures and phase transformations. The ratios of Ni-equivalent (Ni, Cu, Pd) and Ti-equivalent (Ti, Zr, Hf) elements in HE-SMAs were varied to establish systems that correspond to stoichiometric, under- and over-stoichiometric binary alloys. It is shown that basic microstructural features of cast and heat-treated HE-SMAs are inherited from the nine binary X–Y subsystems (X: Ni, Cu, Pd; Y: Ti, Zr, Hf). The phase transition temperatures that characterize the martensitic forward and reverse transformations depend on the concentrations of all alloy elements. The data obtained demonstrate how martensite start temperatures are affected by deviations from the composition of an ideal stoichiometric B2 phase. The findings are discussed in the light of previous work on the concentration dependence of SMA transformation temperatures, and directions for the development of new shape memory alloy compositions are proposed. © 2020 The Author

Two different subunits of importin cooperate to recognize nuclear localization signals and bind them to the nuclear envelope

AbstractBackground: Selective protein import into the cell nucleus occurs in two steps: binding to the nuclear envelope, followed by energy-dependent transit through the nuclear pore complex. A 60 kD protein, importin, is essential for the first nuclear import step, and the small G protein Ran/TC4 is essential for the second. We have previously purified the 60 kD importin protein (importin 60) as a single polypeptide.Results We have identified importin 90, a 90 kD second subunit that dissociates from importin 60 during affinity chromatography on nickel (II)–nitrolotriacetic acid–Sepharose, a technique that was originally used to purify importin 60. Partial amino-acid sequencing of Xenopus importin 90 allowed us to clone and sequence its human homologue; the amino-acid sequence of importin 90 is strikingly conserved between the two species. We have also identified a homologous budding yeast sequence from a database entry. Importin 90 potentiates the effects of importin 60 on nuclear protein import, indicating that the importin complex is the physiological unit responsible for import. To assess whether nuclear localization sequences are recognized by cytosolic receptor proteins, a biotin-tagged conjugate of nuclear localization signals linked to bovine serum albumin was allowed to form complexes with cytosolic proteins in Xenopus egg extracts; the complexes were then retrieved with streptavidin–agarose. The pattern of bound proteins was surprisingly simple and showed only two predominant bands: those of the importin complex. We also expressed the human homologue of importin 60, Rch1p, and found that it was able to replace its Xenopus counterpart in a functional assay. We discuss the relationship of importin 60 and importin 90 to other nuclear import factors.Conclusion Importin consists of a 60 and a 90 kD subunit. Together, they constitute a cytosolic receptor for nuclear localization signals that enables import substrates to bind to the nuclear envelope

Secondary mineral formation associated with respiration of nontronite, NAu-1 by iron reducing bacteria

Experimental batch and miscible-flow cultures were studied in order to determine the mechanistic pathways of microbial Fe(III) respiration in ferruginous smectite clay, NAu-1. The primary purpose was to resolve if alteration of smectite and release of Fe precedes microbial respiration. Alteration of NAu-1, represented by the morphological and mineralogical changes, occurred regardless of the extent of microbial Fe(III) reduction in all of our experimental systems, including those that contained heat-killed bacteria and those in which O(2), rather than Fe(III), was the primary terminal electron acceptor. The solid alteration products observed under transmission electron microscopy included poorly crystalline smectite with diffuse electron diffraction signals, discrete grains of Fe-free amorphous aluminosilicate with increased Al/Si ratio, Fe-rich grains, and amorphous Si globules in the immediate vicinity of bacterial cells and extracellular polymeric substances. In reducing systems, Fe was also found as siderite. The small amount of Fe partitioned to the aqueous phase was primarily in the form of dissolved Fe(III) species even in the systems in which Fe(III) was the primary terminal electron acceptor for microbial respiration. From these observations, we conclude that microbial respiration of Fe(III) in our laboratory systems proceeded through the following: (1) alteration of NAu-1 and concurrent release of Fe(III) from the octahedral sheets of NAu-1; and (2) subsequent microbial respiration of Fe(III)

Deformation-Induced Martensite: A New Paradigm for Exceptional Steels

Atom-probe tomography (APT) and synchrotron X-ray diffraction (XRD) were combined to study the carbon supersaturation of ferrite for two pearlitic steel-wire compositions, eutectoid and hypereutectoid. The samples were cold-drawn at different strains up to true drawing strains for the eutectoid steel and the hypereutectoid steel, respectively. The wire diameters range from 1.7 mm down to 0.058 mm for the eutectoid steel and from 0.54 mm down to 0.02 mm for the hypereutectoid steel. The findings reveal that cold-drawing of pearlitic steel wires leads to a carbon-supersaturated ferrite causing a spontaneous tetragonal distortion of the ferrite unit cell through a strain-induced deformation driven martensitic transformation. We fi nd that the drawing process induced a significant increase in the carbon content inside the originally nearcarbon-free ferrite until a steady state is approached at drawing strains larger than ca. 4 for the wires. The change of carbon concentration in the ferrite grains during the drawing process is closely related to the tetragonal distortion of the ferrite unit cell

Bactericidal Efficacy of Cold Plasma at Different Depths of Infected Root Canals In Vitro

Objectives: Cold plasma (CP) has been shown to be effective even against multiresistant microorganisms. As previous investigations on the effect of CP in root canals showed promising results, the aim of the present study was to analyze the bactericidal efficacy of CP in different depths of infected dentin. Methods: 32 standardized root canals of human mandibular premolars were infected with Enterococcus faecalis and incubated for one week. Specimens were randomly selected for one of four disinfection methods: control (5mL NaCl), 5mL chlorhexidine (CHX), CP alone (CP), and a combination of 5mL CHX and cold plasma (CHX+CP). CHX was ultrasonically activated for 30s, while cold plasma was used for 60s in the root canals. Dentin samples at depths of 300, 500 and 800 µm were obtained and diluted serially. Colony forming units (CFUs) were counted on agar plates after 24h of incubation. Results: The highest overall logarithmic reduction factors (RF) were obtained from CHX+CP (log RF 3.56 p<0.01; Mann-Whitney U test), followed by CP (log RF 3.27 p<0.01) and CHX alone (log RF 2.65 p<0.01) related to the control. All disinfection methods showed significantly lower CFU counts compared to the control group in 300 µm and 800 µm (both p<0.01, Kruskal-Wallis test). Discussion: The adjuvant use of CP might be beneficial in highly infected root canals to improved disinfection. However, the disinfection effect against Enterococcus faecalis of CP is comparable to ultrasonically activated CHX

A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes

GC-biased gene conversion (gBGC) is a recombination-associated process that favors the fixation of G/C alleles over A/T alleles. In mammals, gBGC is hypothesized to contribute to variation in GC content, rapidly evolving sequences, and the fixation of deleterious mutations, but its prevalence and general functional consequences remain poorly understood. gBGC is difficult to incorporate into models of molecular evolution and so far has primarily been studied using summary statistics from genomic comparisons. Here, we introduce a new probabilistic model that captures the joint effects of natural selection and gBGC on nucleotide substitution patterns, while allowing for correlations along the genome in these effects. We implemented our model in a computer program, called phastBias, that can accurately detect gBGC tracts about 1 kilobase or longer in simulated sequence alignments. When applied to real primate genome sequences, phastBias predicts gBGC tracts that cover roughly 0.3% of the human and chimpanzee genomes and account for 1.2% of human-chimpanzee nucleotide differences. These tracts fall in clusters, particularly in subtelomeric regions; they are enriched for recombination hotspots and fast-evolving sequences; and they display an ongoing fixation preference for G and C alleles. They are also significantly enriched for disease-associated polymorphisms, suggesting that they contribute to the fixation of deleterious alleles. The gBGC tracts provide a unique window into historical recombination processes along the human and chimpanzee lineages. They supply additional evidence of long-term conservation of megabase-scale recombination rates accompanied by rapid turnover of hotspots. Together, these findings shed new light on the evolutionary, functional, and disease implications of gBGC. The phastBias program and our predicted tracts are freely available. © 2013 Capra et al

Interleukin 1α Promotes Th1 Differentiation and Inhibits Disease Progression in Leishmania major–susceptible BALB/c Mice

Protective immunity against pathogens such as Leishmania major is mediated by interleukin (IL)-12–dependent Th1-immunity. We have shown previously that skin-dendritic cells (DCs) from both resistant C57BL/6 and susceptible BALB/c mice release IL-12 when infected with L. major, and infected BALB/c DCs effectively vaccinate against leishmaniasis. To determine if cytokines other than IL-12 might influence disease outcome, we surveyed DCs from both strains for production of a variety of cytokines. Skin-DCs produced significantly less IL-1α in response to lipopolysaccharide/interferon γ or L. major when expanded from BALB/c as compared with C57BL/6 mice. In addition, IL-1α mRNA accumulation in lymph nodes of L. major–infected BALB/c mice was ∼3-fold lower than that in C57BL/6 mice. Local injections of IL-1α during the first 3 d after infection led to dramatic, persistent reductions in lesion sizes. In L. major–infected BALB/c mice, IL-1α administration resulted in increased Th1- and strikingly decreased Th2-cytokine production. IL-1α and IL-12 treatments were similarly effective, and IL-1α efficacy was strictly IL-12 dependent. These data indicate that transient local administration of IL-1α acts in conjunction with IL-12 to influence Th-development in cutaneous leishmaniasis and prevents disease progression in susceptible BALB/c mice, perhaps by enhancing DC-induced Th1-education. Differential production of IL-1 by C57BL/6 and BALB/c mice may provide a partial explanation for the disparate outcomes of infection in these mouse strains