Estabilidade de agregados, distribuição e perda de carbono em um latossolo vermelho amarelo sob diferentes manejos no bioma Amazônia.

O objetivo deste estudo foi avaliar as alterações causadas na estabilidade de agregados, distribuição e perda de C em agregados em solo submetido a sistemas exclusivos de cultivo em comparação ao sistema de integração lavoura-pecuária-floresta.. As avaliações foram realizadas em Sinop-MT, em Latossolo Vermelho Amarelo. Os tratamentos foram: Floresta: (floresta plantada com eucalipto); Lavoura: (lavoura com sucessão soja na safra e milho segunda safra consorciado com braquiária); Pastagem: (pastagem de B. brizantha (U. brizantha) cv Marandu); ILPF: (sistema integração lavoura-pecuária-floresta com floresta de eucalipto e cultivo entre renques de soja na safra e milho consorciado com pasto na segunda safra). O delineamento utilizado foi de blocos ao acaso com quatro repetições. Para as análises de estabilidade de agregados e distribuição de carbono foram retiradas de cada tratamento amostras indeformadas (monólitos), nas camadas de 0-5 cm, 5-10 cm e 10-20 cm. Ao analisar os agregados não foram observadas diferenças para DMP (diâmetro médio ponderado) e DMG (diâmetro médio geométrico) nas camadas de 0-5 e 10-20 cm. Porém, na camada de 5-10 cm o tratamento pastagem mostrou os maiores DMP (4,91 mm) e DMG (3,35 mm). As classes de agregados retidas nas peneiras 1,00 e 0,50 mm apresentaram os maiores teores de C nas três camadas estudadas, porém entre manejos não houve diferença significativa. No período considerado, apenas o DMG foi sensível às mudanças ocasionadas pelo sistema ILPF na camada superficial ao longo das distâncias dos renques de árvores. Após três anos de implantação, o sistema ILPF não promoveu alterações na agregação do solo comparado com os cultivos exclusivos.Dissertação (Mestrado em Agronomia) ­- Universidade Federal de Mato Grosso. Orientador: Eduardo da Silva Matos, CPAMT

Assembly of viral genomes from metagenomes

Viral infections remain a serious global health issue. Metagenomic approaches are increasingly used in the detection of novel viral pathogens but also to generate complete genomes of uncultivated viruses. In silico identification of complete viral genomes from sequence data would allow rapid phylogenetic characterization of these new viruses. Often, however, complete viral genomes are not recovered, but rather several distinct contigs derived from a single entity are, some of which have no sequence homology to any known proteins. De novo assembly of single viruses from a metagenome is challenging, not only because of the lack of a reference genome, but also because of intrapopulation variation and uneven or insufficient coverage. Here we explored different assembly algorithms, remote homology searches, genome-specific sequence motifs, k-mer frequency ranking, and coverage profile binning to detect and obtain viral target genomes from metagenomes. All methods were tested on 454-generated sequencing datasets containing three recently described RNA viruses with a relatively large genome which were divergent to previously known viruses from the viral families Rhabdoviridae and Coronaviridae. Depending on specific characteristics of the target virus and the metagenomic community, different assembly and in silico gap closure strategies were successful in obtaining near complete viral genomes.This work was partially funded by the Virgo Consortium, funded by the Dutch government project number FES0908, by Netherlands Genomics Initiative (NGI) project number 050-060-452 and ZonMW TOP project 91213058. A. Ruiz-Gonzalez holds a Post doc fellowship awarded by the Department of Education, Universities and Research of the Basque Government (Ref. DKR-2012-64) and was partially supported by the Research group on "Systematics, Biogeography and Population Dynamics" (Basque Government; Ref. IT317-10; GIC10/76)

Corrections to scaling in 2--dimensional polymer statistics

Writing $= AN^{2\nu}(1+BN^{-\Delta_1}+CN^{-1}+ ...)$ for the mean square end--to--end length $$ of a self--avoiding polymer chain of $N$ links, we have calculated $\Delta_1$ for the two--dimensional {\em continuum} case from a new {\em finite} perturbation method based on the ground state of Edwards self consistent solution which predicts the (exact) $\nu=3/4$ exponent. This calculation yields $\Delta_1=1/2$. A finite size scaling analysis of data generated for the continuum using a biased sampling Monte Carlo algorithm supports this value, as does a re--analysis of exact data for two--dimensional lattices.Comment: 10 pages of RevTex, 5 Postscript figures. Accepted for publication in Phys. Rev. B. Brief Reports. Also submitted to J. Phys.

Scaling of Star Polymers with one to 80 Arms

We present large statistics simulations of 3-dimensional star polymers with up to $f=80$ arms, and with up to 4000 monomers per arm for small values of $f$. They were done for the Domb-Joyce model on the simple cubic lattice. This is a model with soft core exclusion which allows multiple occupancy of sites but punishes each same-site pair of monomers with a Boltzmann factor $v<1$. We use this to allow all arms to be attached at the central site, and we use the `magic' value $v=0.6$ to minimize corrections to scaling. The simulations are made with a very efficient chain growth algorithm with resampling, PERM, modified to allow simultaneous growth of all arms. This allows us to measure not only the swelling (as observed from the center-to-end distances), but also the partition sum. The latter gives very precise estimates of the critical exponents $\gamma_f$. For completeness we made also extensive simulations of linear (unbranched) polymers which give the best estimates for the exponent $\gamma$.Comment: 7 pages, 7 figure

Pathological findings in the red fox (Vulpes vulpes), stone marten (Martes foina) and raccoon dog (Nyctereutes procyonoides), with special emphasis on infectious and zoonotic agents in Northern Germany

Anthropogenic landscape changes contributed to the reduction of availability of habitats to wild animals. Hence, the presence of wild terrestrial carnivores in urban and peri-urban sites has increased considerably over the years implying an increased risk of interspecies spillover of infectious diseases and the transmission of zoonoses. The present study provides a detailed characterisation of the health status of the red fox (Vulpes vulpes), stone marten (Martes foina) and raccoon dog (Nyctereutes procyonoides) in their natural rural and periurban habitats in Schleswig-Holstein, Germany between November 2013 and January 2016 with focus on zoonoses and infectious diseases that are potentially threatening to other wildlife or domestic animal species. 79 red foxes, 17 stone martens and 10 raccoon dogs were collected from traps or hunts. In order to detect morphological changes and potential infectious diseases, necropsy and pathohistological work-up was performed. Additionally, in selected animals immunohistochemistry (influenza A virus, parvovirus, feline leukemia virus, Borna disease virus, tick-borne encephalitis, canine adenovirus, Neospora caninum, Toxoplasma gondii and Listeria monocytogenes), next-generation sequencing, polymerase chain reaction (fox circovirus) and serum-neutralisation analysis (canine distemper virus) were performed. Furthermore, all animals were screened for fox rabies virus (immunofluorescence), canine distemper virus (immunohistochemistry) and Aujeszky's disease (virus cultivation). The most important findings included encephalitis (n = 16) and pneumonia (n =20). None of the investigations revealed a specific cause for the observed morphological alterations except for one animal with an elevated serum titer of 1:160 for canine distemper. Animals displayed macroscopically and/or histopathologically detectable infections with parasites, including Taenia sp., Toxocara sp. and Alaria alata. In summary, wildlife predators carry zoonotic parasitic disease and suffer from inflammatory diseases of yet unknown etiology, possibly bearing infectious potential for other animal species and humans. This study highlights the value of monitoring terrestrial wildlife following the "One Health" notion, to estimate the incidence and the possible spread of zoonotic pathogens and to avoid animal to animal spillover as well as transmission to humans

Statistical Mechanics of Membrane Protein Conformation: A Homopolymer Model

The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\alpha$-helix integration into the membrane that results depending upon membrane permeability and polymer adsorptivity. For a membrane with the permeability larger than a critical value, the integration becomes the second order transition that occurs at the same temperature as that of the adsorption transition. For a nonadsorbing membrane, the integration is of the first order due to the aggregation of $\alpha$-helices.Comment: RevTeX with 5 postscript figure

Critical Exponents, Hyperscaling and Universal Amplitude Ratios for Two- and Three-Dimensional Self-Avoiding Walks

We make a high-precision Monte Carlo study of two- and three-dimensional self-avoiding walks (SAWs) of length up to 80000 steps, using the pivot algorithm and the Karp-Luby algorithm. We study the critical exponents $\nu$ and $2\Delta_4 -\gamma$ as well as several universal amplitude ratios; in particular, we make an extremely sensitive test of the hyperscaling relation $d\nu = 2\Delta_4 -\gamma$. In two dimensions, we confirm the predicted exponent $\nu = 3/4$ and the hyperscaling relation; we estimate the universal ratios $\ / \ = 0.14026 \pm 0.00007$, $\ / \ = 0.43961 \pm 0.00034$ and $\Psi^* = 0.66296 \pm 0.00043$ (68\% confidence limits). In three dimensions, we estimate $\nu = 0.5877 \pm 0.0006$ with a correction-to-scaling exponent $\Delta_1 = 0.56 \pm 0.03$ (subjective 68\% confidence limits). This value for $\nu$ agrees excellently with the field-theoretic renormalization-group prediction, but there is some discrepancy for $\Delta_1$. Earlier Monte Carlo estimates of $\nu$, which were $\approx\! 0.592$, are now seen to be biased by corrections to scaling. We estimate the universal ratios $\ / \ = 0.1599 \pm 0.0002$ and $\Psi^* = 0.2471 \pm 0.0003$; since $\Psi^* > 0$, hyperscaling holds. The approach to $\Psi^*$ is from above, contrary to the prediction of the two-parameter renormalization-group theory. We critically reexamine this theory, and explain where the error lies.Comment: 87 pages including 12 figures, 1029558 bytes Postscript (NYU-TH-94/09/01

Strategies of the honeybee Apis mellifera during visual search for vertical targets presented at various heights: a role for spatial attention?

When honeybees are presented with a colour discrimination task, they tend to choose swiftly and accurately when objects are presented in the ventral part of their frontal visual field. In contrast, poor performance is observed when objects appear in the dorsal part. Here we investigate if this asymmetry is caused by fixed search patterns or if bees can use alternative search mechanisms such as spatial attention, which allows flexible focusing on different areas of the visual field. We asked individual honeybees to choose an orange rewarded target among blue distractors. Target and distractors were presented in the ventral visual field, the dorsal field or both. Bees presented with targets in the ventral visual field consistently had the highest search efficiency, with rapid decisions, high accuracy and direct flight paths. In contrast, search performance for dorsally located targets was inaccurate and slow at the beginning of the test phase, but bees increased their search performance significantly after a few learning trials: they found the target faster, made fewer errors and flew in a straight line towards the target. However, bees needed thrice as long to improve the search for a dorsally located target when the target's position changed randomly between the ventral and the dorsal visual field. We propose that honeybees form expectations of the location of the target's appearance and adapt their search strategy accordingly. Different possible mechanisms of this behavioural adaptation are discussed.L.M. was recipient of a DOC-fFORTE fellowship of the Austrian Academy of Science at the Department of Integrative Zoology, University of Vienna. L.C. is supported by an ERC Advanced Grant and a Royal Society Wolfson Research Merit Award

Preclinical immunogenicity and protective efficacy of a SARS-CoV-2 RBD-based vaccine produced with the thermophilic filamentous fungal expression system Thermothelomyces heterothallica C1

INTRODUCTION: The emergency use of vaccines has been the most efficient way to control the coronavirus disease 19 (COVID-19) pandemic. However, the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern has reduced the efficacy of currently used vaccines. The receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein is the main target for virus neutralizing (VN) antibodies. METHODS: A SARS-CoV-2 RBD vaccine candidate was produced in the Thermothelomyces heterothallica (formerly, Myceliophthora thermophila) C1 protein expression system and coupled to a nanoparticle. Immunogenicity and efficacy of this vaccine candidate was tested using the Syrian golden hamster (Mesocricetus auratus) infection model. RESULTS: One dose of 10-μg RBD vaccine based on SARS-CoV-2 Wuhan strain, coupled to a nanoparticle in combination with aluminum hydroxide as adjuvant, efficiently induced VN antibodies and reduced viral load and lung damage upon SARS-CoV-2 challenge infection. The VN antibodies neutralized SARS-CoV-2 variants of concern: D614G, Alpha, Beta, Gamma, and Delta. DISCUSSION: Our results support the use of the Thermothelomyces heterothallica C1 protein expression system to produce recombinant vaccines against SARS-CoV-2 and other virus infections to help overcome limitations associated with the use of mammalian expression system