Genome sequences of five Lactobacillus sp. isolates from traditional Turkish sourdough

A high level of variation in microflora can be observed in profiles of lactic acid bacteria (LAB) from sourdoughs. Here, we present draft genome sequences of Lactobacillus reuteri E81, L. reuteri LR5A, L. rhamnosus LR2, L. plantarum PFC-311, and the novel Lactobacillus sp. strain PFC-70, isolated from traditional Turkish backslopped wheat sourdoughs. © 2018 Dertli et al

A New Greek Graffito from the Bilsk Hillfort and Greek Graffiti in Scythian Contexts

The article presents a recent find of a potsherd, bearing an ancient Greek graffito, reported from the area of the Bilsk Hillfort. The area of discovery, considered by some archaeologists to be the city of Gelonos (Hdt. 4.108), makes this otherwise ordinary graffito potentially significant. The authors discuss the historical, archaeological, and epigraphic contexts of the find and possible scenarios of how it may have ended up at the site. To provide an epigraphic background for the find, the study is accompanied by a catalogue of Greek graffiti and dipinti from Scythian burials and settlements of the Northern Black Sea area and steppe and forest-steppe zones of Eastern Europe

Fob1 and Fob2 Proteins Are Virulence Determinants of Rhizopus oryzae via Facilitating Iron Uptake from Ferrioxamine.

Dialysis patients with chronic renal failure receiving deferoxamine for treating iron overload are uniquely predisposed for mucormycosis, which is most often caused by Rhizopus oryzae. Although the deferoxamine siderophore is not secreted by Mucorales, previous studies established that Rhizopus species utilize iron from ferrioxamine (iron-rich form of deferoxamine). Here we determined that the CBS domain proteins of Fob1 and Fob2 act as receptors on the cell surface of R. oryzae during iron uptake from ferrioxamine. Fob1 and Fob2 cell surface expression was induced in the presence of ferrioxamine and bound radiolabeled ferrioxamine. A R. oryzae strain with targeted reduced Fob1/Fob2 expression was impaired for iron uptake, germinating, and growing on medium with ferrioxamine as the sole source of iron. This strain also exhibited reduced virulence in a deferoxamine-treated, but not the diabetic ketoacidotic (DKA), mouse model of mucormycosis. The mechanism by which R. oryzae obtains iron from ferrioxamine involves the reductase/permease uptake system since the growth on ferrioxamine supplemented medium is associated with elevated reductase activity and the use of the ferrous chelator bathophenanthroline disulfonate abrogates iron uptake and growth on medium supplemented with ferrioxamine as a sole source of iron. Finally, R. oryzae mutants with reduced copies of the high affinity iron permease (FTR1) or with decreased FTR1 expression had an impaired iron uptake from ferrioxamine in vitro and reduced virulence in the deferoxamine-treated mouse model of mucormycosis. These two receptors appear to be conserved in Mucorales, and can be the subject of future novel therapy to maintain the use of deferoxamine for treating iron-overload

Optimized Multi-Frequency Spectra for Applications in Radiative Feedback and Cosmological Reionization

The recent implementation of radiative transfer algorithms in numerous hydrodynamics codes has led to a dramatic improvement in studies of feedback in various astrophysical environments. However, because of methodological limitations and computational expense, the spectra of radiation sources are generally sampled at only a few evenly-spaced discrete emission frequencies. Using one-dimensional radiative transfer calculations, we investigate the discrepancies in gas properties surrounding model stars and accreting black holes that arise solely due to spectral discretization. We find that even in the idealized case of a static and uniform density field, commonly used discretization schemes induce errors in the neutral fraction and temperature by factors of two to three on average, and by over an order of magnitude in certain column density regimes. The consequences are most severe for radiative feedback operating on large scales, dense clumps of gas, and media consisting of multiple chemical species. We have developed a method for optimally constructing discrete spectra, and show that for two test cases of interest, carefully chosen four-bin spectra can eliminate errors associated with frequency resolution to high precision. Applying these findings to a fully three-dimensional radiation-hydrodynamic simulation of the early universe, we find that the HII region around a primordial star is substantially altered in both size and morphology, corroborating the one-dimensional prediction that discrete spectral energy distributions can lead to sizable inaccuracies in the physical properties of a medium, and as a result, the subsequent evolution and observable signatures of objects embedded within it.Comment: 15 pages, 13 figures, 2 tables, accepted for publication in the Astrophysical Journa

Parallel HOP: A Scalable Halo Finder for Massive Cosmological Data Sets

Modern N-body cosmological simulations contain billions ($10^9$) of dark matter particles. These simulations require hundreds to thousands of gigabytes of memory, and employ hundreds to tens of thousands of processing cores on many compute nodes. In order to study the distribution of dark matter in a cosmological simulation, the dark matter halos must be identified using a halo finder, which establishes the halo membership of every particle in the simulation. The resources required for halo finding are similar to the requirements for the simulation itself. In particular, simulations have become too extensive to use commonly-employed halo finders, such that the computational requirements to identify halos must now be spread across multiple nodes and cores. Here we present a scalable-parallel halo finding method called Parallel HOP for large-scale cosmological simulation data. Based on the halo finder HOP, it utilizes MPI and domain decomposition to distribute the halo finding workload across multiple compute nodes, enabling analysis of much larger datasets than is possible with the strictly serial or previous parallel implementations of HOP. We provide a reference implementation of this method as a part of the toolkit yt, an analysis toolkit for Adaptive Mesh Refinement (AMR) data that includes complementary analysis modules. Additionally, we discuss a suite of benchmarks that demonstrate that this method scales well up to several hundred tasks and datasets in excess of $2000^3$ particles. The Parallel HOP method and our implementation can be readily applied to any kind of N-body simulation data and is therefore widely applicable.Comment: 29 pages, 11 figures, 2 table

Metabolic engineering of Rhizopus oryzae for the production of platform chemicals

Rhizopus oryzae is a filamentous fungus belonging to the Zygomycetes. It is among others known for its ability to produce the sustainable platform chemicals l-(+)-lactic acid, fumaric acid, and ethanol. During glycolysis, all fermentable carbon sources are metabolized to pyruvate and subsequently distributed over the pathways leading to the formation of these products. These platform chemicals are produced in high yields on a wide range of carbon sources. The yields are in excess of 85 % of the theoretical yield for l-(+)-lactic acid and ethanol and over 65 % for fumaric acid. The study and optimization of the metabolic pathways involved in the production of these compounds requires well-developed metabolic engineering tools and knowledge of the genetic makeup of this organism. This review focuses on the current metabolic engineering techniques available for R. oryzae and their application on the metabolic pathways of the main fermentation products

A Multi-Code Analysis Toolkit for Astrophysical Simulation Data

The analysis of complex multiphysics astrophysical simulations presents a unique and rapidly growing set of challenges: reproducibility, parallelization, and vast increases in data size and complexity chief among them. In order to meet these challenges, and in order to open up new avenues for collaboration between users of multiple simulation platforms, we present yt (available at http://yt.enzotools.org/), an open source, community-developed astrophysical analysis and visualization toolkit. Analysis and visualization with yt are oriented around physically relevant quantities rather than quantities native to astrophysical simulation codes. While originally designed for handling Enzo's structure adaptive mesh refinement (AMR) data, yt has been extended to work with several different simulation methods and simulation codes including Orion, RAMSES, and FLASH. We report on its methods for reading, handling, and visualizing data, including projections, multivariate volume rendering, multi-dimensional histograms, halo finding, light cone generation and topologically-connected isocontour identification. Furthermore, we discuss the underlying algorithms yt uses for processing and visualizing data, and its mechanisms for parallelization of analysis tasks.Comment: 18 pages, 6 figures, emulateapj format. Resubmitted to Astrophysical Journal Supplement Series with revisions from referee. yt can be found at http://yt.enzotools.org

The Nature of the Warm/Hot Intergalactic Medium I. Numerical Methods, Convergence, and OVI Absorption

We perform a series of cosmological simulations using Enzo, an Eulerian adaptive-mesh refinement, N-body + hydrodynamical code, applied to study the warm/hot intergalactic medium. The WHIM may be an important component of the baryons missing observationally at low redshift. We investigate the dependence of the global star formation rate and mass fraction in various baryonic phases on spatial resolution and methods of incorporating stellar feedback. Although both resolution and feedback significantly affect the total mass in the WHIM, all of our simulations find that the WHIM fraction peaks at z ~ 0.5, declining to 35-40% at z = 0. We construct samples of synthetic OVI absorption lines from our highest-resolution simulations, using several models of oxygen ionization balance. Models that include both collisional ionization and photoionization provide excellent fits to the observed number density of absorbers per unit redshift over the full range of column densities (10^13 cm-2 <= N_OVI <= 10^15 cm^-2). Models that include only collisional ionization provide better fits for high column density absorbers (N_OVI > 10^14 cm^-2). The distribution of OVI in density and temperature exhibits two populations: one at T ~ 10^5.5 K (collisionally ionized, 55% of total OVI) and one at T ~ 10^4.5 K (photoionized, 37%) with the remainder located in dense gas near galaxies. While not a perfect tracer of hot gas, OVI provides an important tool for a WHIM baryon census.Comment: 22 pages, 21 figures, emulateapj, accepted for publication in Ap

The nuclear lamina couples mechanical forces to cell fate in the preimplantation embryo via actin organization

During preimplantation development, contractile forces generated at the apical cortex segregate cells into inner and outer positions of the embryo, establishing the inner cell mass (ICM) and trophectoderm. To which extent these forces influence ICM-trophectoderm fate remains unresolved. Here, we found that the nuclear lamina is coupled to the cortex via an F-actin meshwork in mouse and human embryos. Actomyosin contractility increases during development, upregulating Lamin-A levels, but upon internalization cells lose their apical cortex and downregulate Lamin-A. Low Lamin-A shifts the localization of actin nucleators from nucleus to cytoplasm increasing cytoplasmic F-actin abundance. This results in stabilization of Amot, Yap phosphorylation and acquisition of ICM over trophectoderm fate. By contrast, in outer cells, Lamin-A levels increase with contractility. This prevents Yap phosphorylation enabling Cdx2 to specify the trophectoderm. Thus, forces transmitted to the nuclear lamina control actin organization to differentially regulate the factors specifying lineage identity