Comparison of Microbial Diversity of Fifteen Aged Cheddar Cheeses from Different Regions Using Next Generation Sequencing

This project was funded by BUILD Dairy to test the efficacy of using next generation sequencing to study Cheddar cheese microbiomes. The 15 different cheese samples used in this study were purchased in the retail market from various manufacturers and different origins of manufacture. Sequencing was done by the Center for Integrated Biosystems at Utah State University using Illumina MiSeq. The aim of this project is to provide further understanding of how using next generation sequencing can benefit the study of bacterial communities and their influence during the aging process of Cheddar cheese and the possibility of identifying defect causing microorganisms. We tested Cheddar cheese samples microbiota by amplifying and sequencing the hypervariable V4 region of the 16S rRNA. Sequencing data was evaluated using two different denoising pipelines within Qiime 2: Deblur and DADA2. We used variant identification as a method of comparing starter and non-starter lactic acid bacteria in cheeses based on regions and manufacturers. In the data denoised by both methods the samples clustered into two groups separated by the dominant starter lactic acid bacteria (SLAB). DADA2 identified over quadruple the number of amplicon sequence variants (ASVs), which represent a unique sequence within the samples, compared to Deblur. Using Deblur we identified 5 Lactococcus lactis ASVs and 3 Streptococcus thermophilus ASVs compared to DADA2 which identified 34 L. lactis ASVs and 35 St. thermophilus. Thus, it can be said that using DADA2 to denoise Cheddar cheese data provides a more realistic representation of the microbiom

On the Application of a Monolithic Array for Detecting Intensity-Correlated Photons Emitted by Different Source Types

It is not widely appreciated that many subtleties are involved in the accurate measurement of intensity-correlated photons; even for the original experiments of Hanbury Brown and Twiss (HBT). Using a monolithic 4x4 array of single-photon avalanche diodes (SPADs), together with an off-chip algorithm for processing streaming data, we investigate the difficulties of measuring second-order photon correlations g2 in a wide variety of light fields that exhibit dramatically different correlation statistics: a multimode He-Ne laser, an incoherent intensity-modulated lamp-light source and a thermal light source. Our off-chip algorithm treats multiple photon-arrivals at pixel-array pairs, in any observation interval, with photon fluxes limited by detector saturation, in such a way that a correctly normalized g2 function is guaranteed. The impact of detector background correlations between SPAD pixels and afterpulsing effects on second-order coherence measurements is discussed. These results demonstrate that our monolithic SPAD array enables access to effects that are otherwise impossible to measure with stand-alone detectors.Comment: 17 pages, 6 figure

Infinite-dimensional diffusions as limits of random walks on partitions

The present paper originated from our previous study of the problem of harmonic analysis on the infinite symmetric group. This problem leads to a family {P_z} of probability measures, the z-measures, which depend on the complex parameter z. The z-measures live on the Thoma simplex, an infinite-dimensional compact space which is a kind of dual object to the infinite symmetric group. The aim of the paper is to introduce stochastic dynamics related to the z-measures. Namely, we construct a family of diffusion processes in the Toma simplex indexed by the same parameter z. Our diffusions are obtained from certain Markov chains on partitions of natural numbers n in a scaling limit as n goes to infinity. These Markov chains arise in a natural way, due to the approximation of the infinite symmetric group by the increasing chain of the finite symmetric groups. Each z-measure P_z serves as a unique invariant distribution for the corresponding diffusion process, and the process is ergodic with respect to P_z. Moreover, P_z is a symmetrizing measure, so that the process is reversible. We describe the spectrum of its generator and compute the associated (pre)Dirichlet form.Comment: AMSTex, 33 pages. Version 2: minor changes, typos corrected, to appear in Prob. Theor. Rel. Field

Variant of TYR and Autoimmunity Susceptibility Loci in Generalized Vitiligo.

BACKGROUND Generalized vitiligo is an autoimmune disease characterized by melanocyte loss, which results in patchy depigmentation of skin and hair, and is associated with an elevated risk of other autoimmune diseases. METHODS To identify generalized vitiligo susceptibility loci, we conducted a genomewide association study. We genotyped 579,146 single-nucleotide polymorphisms (SNPs) in 1514 patients with generalized vitiligo who were of European-derived white (CEU) ancestry and compared the genotypes with publicly available control genotypes from 2813 CEU persons. We then tested 50 SNPs in two replication sets, one comprising 677 independent CEU patients and 1106 CEU controls and the other comprising 183 CEU simplex trios with generalized vitiligo and 332 CEU multiplex families. RESULTS We detected significant associations between generalized vitiligo and SNPs at several loci previously associated with other autoimmune diseases. These included genes encoding major-histocompatibility-complex class I molecules (P=9.05×10−23) and class II molecules (P=4.50×10−34), PTPN22 (P=1.31×10−7), LPP (P=1.01×10−11), IL2RA (P=2.78×10−9), UBASH3A (P=1.26×10−9), and C1QTNF6 (P=2.21×10−16). We also detected associations between generalized vitiligo and SNPs in two additional immune-related loci, RERE (P=7.07×10−15) and GZMB (P=3.44×10−8), and in a locus containing TYR (P=1.60×10−18), encoding tyrosinase. CONCLUSIONS We observed associations between generalized vitiligo and markers implicating multiple genes, some associated with other autoimmune diseases and one (TYR) that may mediate target-cell specificity and indicate a mutually exclusive relationship between susceptibility to vitiligo and susceptibility to melanoma

Common variants in FOXP1 are associated with generalized vitiligo

In a recent genome-wide association study of generalized vitiligo, we identified ten confirmed susceptibility loci. By testing additional loci that showed suggestive association in the genome-wide study, using two replication cohorts of European descent, we observed replicated association of generalized vitiligo with variants at 3p13 encompassing FOXP1 (rs17008723, combined P = 1.04 × 10−8) and with variants at 6q27 encompassing CCR6 (rs6902119, combined P = 3.94 × 10−7)

Os butiazais e as transformações das paisagens na região do Parque Estadual do Podocarpus, Encruzilhada do Sul, RS.

Esta publicação é um produto do projeto Rota dos Butiazais: fortalecimento da cadeia produtiva do butiá associado à recuperação da vegetação nativa na região do Parque Estadual do Podocarpus (Encruzilhada do Sul, RS), e discute o estado de conservação dos butiazais e região do entorno do Parque Estadual do Podocarpus, no município de Encruzilhada do Sul, RS. Foram realizadas atividades com o objetivo de identificar remanescentes de vegetação nativa (campos, butiazais, florestas) na região do Parque Estadual do Podocarpus e arredores e identificar áreas degradadas de campos e butiazais com potencial para restauração ecológica. Este trabalho descreve o uso e cobertura do solo atual (2020) e evidencia as transformações ocorridas nessa cobertura ao longo dos últimos 30 anos (1990 - 2020) na região do Parque Estadual do Podocarpus e arredores, considerando sua zona de amortecimento e os remanescentes de butiazais no município de Encruzilhada do Sul. Elucidar essas transformações e, principalmente, localizá-las espacialmente possibilita definir áreas potenciais para ações de restauração e identificar áreas que seguem sendo cobertas por formações campestres, ou seja, locais potenciais para coleta de sementes de espécies nativas que possam vir a ser utilizadas na recuperação de áreas de campo degradadas no Bioma Pampa.ODS 15

Chiral and herringbone symmetry breaking in water-surface monolayers

We report the observation from monolayers of eicosanoic acid in the L′2 phase of three distinct out-of-plane first-order diffraction peaks, indicating molecular tilt in a nonsymmetry direction and hence the absence of mirror symmetry. At lower pressures the molecules tilt in the direction of their nearest neighbors. In this region we find a structural transition, which we tentatively identify as the rotator-herringbone transition L2d−L2h

Understanding Brazil’s catastrophic fires : causes, consequences and policy needed to prevent future tragedies

Brazil has experienced unprecedented wildfires in the last decade. Images ofimmense burnt areas or dead animals that failed to escape the 2020 wildfires have shocked the world. To prevent or minimize further similardisasters wemustunderstandthe factors thathave ledto these catastrophic events. The causes and consequences of wildfires entail complex interactions between the biophysical and sociocultural spheres, and suitable management decisions require a sound scientific base. We present the recent panorama of increasing fire outbreaks in the Brazilian biomes, and discuss the causes that have contributed to such fires, their impacts on the environment and overall consequences for human well-being, based on reviewing the extensive specialist literature, on authors’ expert knowledge and information provided by environmental managers, researchers and politicians during a workshop organized to debate the wildfire issue in Brazil. Our up-to-date review is aimed at the academic public, environmental managers and decision- and policy-makers. First, we present evidence on the contrasting effects of fire on different ecosystems. Second, we outline the historic perceptions and policies related to fire use and management in Brazil since its colonization to the present date. Third, we propose means to advance fire prevention and develop successful management strategies. Finally, we answer frequently asked questions to clarify and/or demystify some fire-related issues not always properly addressed in the media