Characterization of multicopper oxidase CopA from Pseudomonas putida KT2440 and Pseudomonas fluorescens Pf-5 : Involvement in bacterial lignin oxidation

CopA is a protein formed as part of a copper resistance operon in Pseudomonas syringae pv tomato, but CopA has also been identified from gene library screening as a potential lignin-oxidising enzyme. Few bacterial homologues for bacterial multi-copper laccases have been identified that can assist in lignin degradation. Bioinformatic analysis revealed that copA and copC genes were found in the genomes of bacterial strains capable of lignin oxidation. In this study, CopA enzymes from bacterial strains with lignin oxidation activity, Pseudomonas putida and P. fluorescens, were heterologously expressed and characterised kinetically, and expression of bacterial CopC proteins was also investigated. Purified CopA enzymes were dependent upon exogenous copper (II) ions for activity when expressed under fully aerated conditions, however after expression under microaerobic conditions with copper reconstitution, the activity was independent of copper addition. The CopA enzymes showed activity towards the laccase substrates 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS); syringaldazine (SGZ); guaiacol; 2,6-dimethoxyphenol (DMP) and 2,4-dichlorophenol (DCP). Moreover, CopA proteins were able to oxidise the lignin model compounds guaiacylglycerol-beta-guaiacyl (GGE) and 2,2′-dihydroxy-3,3′-dimethoxy-5,5′-dicarboxybiphenyl (DDVA), giving oxidised dimerised products; and they were active towards Ca-lignosulfonate, giving vanillic acid as product. A double gene deletion of copA-I and copA-II genes in Pseudomonas putida KT2440 was constructed, and this mutant showed diminished growth capability on different small aromatic compounds related with lignin degradation, when copper salts were present in the media

Abrupt field-induced transition triggered by magnetocaloric effect in phase-separated manganites

The occurrence at low temperatures of an ultrasharp field-induced transition in phase separated manganites is analyzed. Experimental results show that magnetization and specific heat step-like transitions below 5 K are correlated with an abrupt change of the sample temperature, which happens at a certain critical field. This temperature rise, a magnetocaloric effect, is interpreted as produced by the released energy at the transition point, and is the key to understand the existence of the abrupt field-induced transition. A qualitative analysis of the results suggests the existence of a critical growing rate of the ferromagnetic phase, beyond which an avalanche effect is triggered.Comment: 6 pages, 4 figures included. Acepted for publication in Phys. Rev.

Structural and energetic properties of nickel clusters: 2≤N≤1502 \le N \le 150

The four most stable structures of Ni$_N$ clusters with $N$ from 2 to 150 have been determined using a combination of the embedded-atom method in the version of Daw, Baskes and Foiles, the {\it variable metric/quasi-Newton} method, and our own {\it Aufbau/Abbau} method. A systematic study of energetics, structure, growth, and stability of also larger clusters has been carried through without more or less severe assumptions on the initial geometries in the structure optimization, on the symmetry, or on bond lengths. It is shown that cluster growth is predominantly icosahedral with $islands$ of {\it fcc}, {\it tetrahedral} and {\it decahedral} growth. For the first time in unbiased computations it is found that Ni$_{147}$ is the multilayer (third Mackay) icosahedron. Further, we point to an enhanced ability of {\it fcc} clusters to compete with the icosahedral and decahedral structures in the vicinity of N=79. In addition, it is shown that conversion from the {\it hcp}/anti-Mackay kind of icosahedral growth to the {\it fcc}/Mackay one occurs within a transition layer including several cluster sizes. Moreover, we present and apply different analytical tools in studying structural and energetic properties of such a large class of clusters. These include means for identifying the overall shape, the occurrence of atomic shells, the similarity of the clusters with, e.g., fragments of the {\it fcc} crystal or of a large icosahedral cluster, and a way of analysing whether the $N$-atom cluster can be considered constructed from the $(N-1)$-atom one by adding an extra atom. In addition, we compare in detail with results from chemical-probe experiment. Maybe the most central result is that first for clusters with $N$ above 80 general trends can be identified.Comment: 37 pages, 11 figure

Late Holocene natural and man induced environmental changes in Western Iberian coast: assessing forcing factors

The Western coast of the Iberian Peninsula stands as an interface between both the Atlantic and Mediterranean climatic influences and marine / fluvial conditions. The paper aims to assess the environmental changes in the last ca 6000 years (both natural and anthropogenic induced) using multiproxy analysis (geomorphological and sedimentological data, elemental and stable isotope content, microfossil assemblages, radiocarbon dating, and historical records) applied to an embayed coast. The results showed the prevalence of marine environment until 6272-6000 cal BP, but with fluvial infilling of the inner embayment, even before present sea level was reached (ca 4500-4000 cal BP). The influx of sediments was probably the result of the four recorded wet episodes (at modelled age cal BP (2σ): E1 – 6067-4770, E2 – 5806-4409, E3 – 5383-4088, and E4 – 4086-3905). These great sediment influxes along the previous 3000 years continues until 2110-1962 cal BP triggering the downstream migration of the river mouth, the development of a sand barrier coast and of a sheltered lagoon inside the palaeo-embayment.Afterwards the sedimentation rate (SR) reached high values (0.19-0.48 cmyr-1), as the result of Roman intervention in the drainage basin where pastures and local fires are recorded, together with an increasing dryness. A major disturbance is recorded in the Pollen Assemblages Zones (between PAZ II and PAZ III) and in the sediments around 1863-1706 cal BP (2σ), in the transition from the Roman Age to the Muslim invasion period, probably reflecting a hiatus in the sedimentary record. Onwards, SR reached 0.21-0.57 cmyr-1. Two major hydro marine episodes may have contributed to this fact: the latter is the Lisbon tsunami (1755 AD) while the former may reflect the 16th Century tsunamis or a great marine storm episode. An aeolian environment prevailed since then and the embayment was transformed into a dune field interrupted only by the narrow channel of the river whose mouth is often closed.info:eu-repo/semantics/publishedVersio

Ising cubes with enhanced surface couplings

Using Monte Carlo techniques, Ising cubes with ferromagnetic nearest-neighbor interactions and enhanced couplings between surface spins are studied. In particular, at the surface transition, the corner magnetization shows non-universal, coupling-dependent critical behavior in the thermodynamic limit. Results on the critical exponent of the corner magnetization are compared to previous findings on two-dimensional Ising models with three intersecting defect lines.Comment: 4 pages, 2 figures included, submitted to Phys. Rev.

Neoplastic Transformation of T Lymphocytes through Transgenic Expression of a Virus Host Modification Protein

Virus host evasion genes are ready-made tools for gene manipulation and therapy. In this work we have assessed the impact in vivo of the evasion gene A238L of the African Swine Fever Virus, a gene which inhibits transcription mediated by both NF-κB and NFAT. The A238L gene has been selectively expressed in mouse T lymphocytes using tissue specific promoter, enhancer and locus control region sequences for CD2. The resulting two independently derived transgenic mice expressed the transgene and developed a metastasic, angiogenic and transplantable CD4+CD8+CD69– lymphoma. The CD4+CD8+CD69– cells also grew vigorously in vitro. The absence of CD69 from the tumour cells suggests that they were derived from T cells at a stage prior to positive selection. In contrast, transgenic mice similarly expressing a mutant A238L, solely inhibiting transcription mediated by NF-κB, were indistinguishable from wild type mice. Expression of Rag1, Rag2, TCRβ-V8.2, CD25, FoxP3, Bcl3, Bcl2 l14, Myc, IL-2, NFAT1 and Itk, by purified CD4+CD8+CD69– thymocytes from A238L transgenic mice was consistent with the phenotype. Similarly evaluated expression profiles of CD4+CD8+ CD69– thymocytes from the mutant A238L transgenic mice were comparable to those of wild type mice. These features, together with the demonstration of (mono-)oligoclonality, suggest a transgene-NFAT-dependent transformation yielding a lymphoma with a phenotype reminiscent of some acute lymphoblastic lymphomas

Transcript-indexed ATAC-seq for precision immune profiling.

T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide-major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples. In peripheral blood CD4+ T cells from healthy individuals, we identified cis and trans regulators of naive and memory T cell states and found substantial heterogeneity in surface-marker-defined T cell populations. In patients with a leukemic form of cutaneous T cell lymphoma, T-ATAC-seq enabled identification of leukemic and nonleukemic regulatory pathways in T cells from the same individual by allowing separation of the signals that arose from the malignant clone from the background T cell noise. Thus, T-ATAC-seq is a new tool that enables analysis of epigenomic landscapes in clonal T cells and should be valuable for studies of T cell malignancy, immunity and immunotherapy

Vibrational Properties of Nanoscale Materials: From Nanoparticles to Nanocrystalline Materials

The vibrational density of states (VDOS) of nanoclusters and nanocrystalline materials are derived from molecular-dynamics simulations using empirical tight-binding potentials. The results show that the VDOS inside nanoclusters can be understood as that of the corresponding bulk system compressed by the capillary pressure. At the surface of the nanoparticles the VDOS exhibits a strong enhancement at low energies and shows structures similar to that found near flat crystalline surfaces. For the nanocrystalline materials an increased VDOS is found at high and low phonon energies, in agreement with experimental findings. The individual VDOS contributions from the grain centers, grain boundaries, and internal surfaces show that, in the nanocrystalline materials, the VDOS enhancements are mainly caused by the grain-boundary contributions and that surface atoms play only a minor role. Although capillary pressures are also present inside the grains of nanocrystalline materials, their effect on the VDOS is different than in the cluster case which is probably due to the inter-grain coupling of the modes via the grain-boundaries.Comment: 10 pages, 7 figures, accepted for publication in Phys. Rev.