Benchmarking urine storage and collection conditions for evaluating the female urinary microbiome.

Standardized conditions for collection, preservation and storage of urine for microbiome research have not been established. We aimed to identify the effects of the use of preservative AssayAssure® (AA), and the effects of storage time and temperatures on reproducibility of urine microbiome results. We sequenced the V3-4 segment of the 16S rRNA gene to characterize the bacterial community in the urine of a cohort of women. Each woman provided a single voided urine sample, which was divided into aliquots and stored with and without AA, at three different temperatures (room temperature [RT], 4 °C, or -20 °C), and for various time periods up to 4 days. There were significant microbiome differences in urine specimens stored with and without AA at all temperatures, but the most significant differences were observed in alpha diversity (estimated number of taxa) at RT. Specimens preserved at 4 °C and -20 °C for up to 4 days with or without AA had no significant alpha diversity differences. However, significant alpha diversity differences were observed in samples stored without AA at RT. Generally, there was greater microbiome preservation with AA than without AA at all time points and temperatures, although not all results were statistically significant. Addition of AA preservative, shorter storage times, and colder temperatures are most favorable for urinary microbiome reproducibility

Physicochemical, antioxidant, and sensorial properties of peach snacks prepared from different cultivars

High potentiality of medicinal benefits of peach have increased its demand, however, supply of fresh fruit to meet the demand is challenging as it grows in specific climatic regions and in particular season. Preparation of varieties of processed peach products could be a good option to supply in lean season. Objective of the study was to assess the quality characteristics of peach snacks prepared from 11 different cultivars. We investigated the physicochemical (soluble solid, titratable acidity, hardness and dry yield), antioxidant (DPPH radical scavenging capacity and total phenolics content) and sensorial properties (color, flavor, texture, sweetness and overall acceptance) of peach snacks prepared from 11 peach cultivars. Peach snacks of different cultivars evaluated in this study showed substantial variations in antioxidant capacity,  physicochemical and sensorial properties. Some of the samples showed higher physicochemical properties while the others contained better antioxidant capacity or sensory properties. Results of this study reveal that quality peach snacks having different properties could be prepared by drying thin slices of fresh fruits of different cultivars. However, supplementary studies on cost effective techniques of peach snacks preparation and variation in nutritive and medicinal properties of processed products could increase the application of the findings of this experiment.Key words: Antioxidant, peach snack, physicochemical, sensory property

New players in the interaction between beetle polygalacturonases and plant polygalacturonase-inhibiting proteins: Insights from proteomics and gene expression analyses

Plants possess various defense strategies to counter attacks from microorganisms or herbivores. For example, plants reduce the cell-wall-macerating activity of pathogen- or insect-derived polygalacturonases (PGs) by expressing PG-inhibiting proteins (PGIPs). PGs and PGIPs belong to multi-gene families believed to have been shaped by an evolutionary arms race. The mustard leaf beetle Phaedon cochleariae expresses both active PGs and catalytically inactive PG pseudoenzymes. Previous studies demonstrated that (i) PGIPs target beetle PGs and (ii) the role of PG pseudoenzymes remains elusive, despite having been linked to the pectin degradation pathway. For further insight into the interaction between plant PGIPs and beetle PG family members, we combined affinity purification with proteomics and gene expression analyses, and identified novel inhibitors of beetle PGs from Chinese cabbage (Brassica rapa ssp. pekinensis). A beetle PG pseudoenzyme was not targeted by PGIPs, but instead interacted with PGIP-like proteins. Phylogenetic analysis revealed that PGIP-like proteins clustered apart from “classical” PGIPs but together with proteins, which have been involved in developmental processes. Our results indicate that PGIP-like proteins represent not only interesting novel PG inhibitor candidates in addition to “classical” PGIPs, but also fascinating new players in the arms race between herbivorous beetles and plant defenses

Kondo-like behaviors in magnetic and thermal properties of single crystal Tm5Si2Ge2

We grew the single crystal of stoichiometric Tm5Si2.0Ge2.0 using a Bridgeman method and performed XRD, EDS, magnetization, ac and dc magnetic susceptibilities, specific heat, electrical resistivity and XPS experiments. It crystallizes in orthorhombic Sm5Ge4-type structure. The mean valence of Tm ions in Tm5Si2.0Ge2.0 is almost trivalent. The 4f states is split by the crystalline electric field. The ground state exhibits the long range antiferromagnetic order with the ferromagnetically coupled magnetic moments in the ac plane below 8.01 K, while the exited states exhibit the reduction of magnetic moment and magnetic entropy and -log T-behaviors observed in Kondo materials.Comment: 8 pages, 13 figure

Tunneling anisotropic magnetoresistance in multilayer-(Co/Pt)/AlOx/Pt structures

We report observations of tunneling anisotropic magnetoresitance (TAMR) in vertical tunnel devices with a ferromagnetic multilayer-(Co/Pt) electrode and a non-magnetic Pt counter-electrode separated by an AlOx barrier. In stacks with the ferromagnetic electrode terminated by a Co film the TAMR magnitude saturates at 0.15% beyond which it shows only weak dependence on the magnetic field strength, bias voltage, and temperature. For ferromagnetic electrodes terminated by two monolayers of Pt we observe order(s) of magnitude enhancement of the TAMR and a strong dependence on field, temperature and bias. Discussion of experiments is based on relativistic ab initio calculations of magnetization orientation dependent densities of states of Co and Co/Pt model systems.Comment: 4 pages, 5 figures, to be published in Phys. Rev. Let

Optimization of sample preparation and green color imaging using the mNeonGreen fluorescent protein in bacterial cells for photoactivated localization microscopy.

mNeonGreen fluorescent protein is capable of photo-switching, hence in principle applicable for super-resolution imaging. However, difficult-to-control blinking kinetics that lead to simultaneous emission of multiple nearby mNeonGreen molecules impedes its use for PALM. Here, we determined the on- and off- switching rate and the influence of illumination power on the simultaneous emission. Increasing illumination power reduces the probability of simultaneous emission, but not enough to generate high quality PALM images. Therefore, we introduce a simple data post-processing step that uses temporal and spatial information of molecule localizations to further reduce artifacts arising from simultaneous emission of nearby emitters. We also systematically evaluated various sample preparation steps to establish an optimized protocol to preserve cellular morphology and fluorescence signal. In summary, we propose a workflow for super-resolution imaging with mNeonGreen based on optimization of sample preparation, data acquisition and simple post-acquisition data processing. Application of our protocol enabled us to resolve the expected double band of bacterial cell division protein DivIVA, and to visualize that the chromosome organization protein ParB organized into sub-clusters instead of the typically observed diffraction-limited foci. We expect that our workflow allows a broad use of mNeonGreen for super-resolution microscopy, which is so far difficult to achieve

Characterization of developmental defects in the forebrain resulting from hyperactivated mTOR signaling by integrative analysis of transcriptomic and proteomic data

Hyperactivated mTOR signaling in the developing brain has been implicated in multiple forms of pathology including tuberous sclerosis complex (TSC). To date, various phenotypic defects such as cortical lamination irregularity, subependymal nodule formation, dysmorphic astrocyte differentiation and dendritic malformation have been described for patients and animal models. However, downstream networks affected in the developing brain by hyperactivated mTOR signaling have yet to be characterized. Here, we present an integrated analysis of transcriptomes and proteomes generated from wild-type and Tsc1/Emx1-Cre forebrains. This led to comprehensive lists of genes and proteins whose expression levels were altered by hyperactivated mTOR signaling. Further incorporation of TSC patient data followed by functional enrichment and network analyses pointed to changes in molecular components and cellular processes associated with neuronal differentiation and morphogenesis as the key downstream events underlying developmental and morphological defects in TSC. Our results provide novel and fundamental molecular bases for understanding hyperactivated mTOR signaling-induced brain defects which can in turn facilitate identification of potential diagnostic markers and therapeutic targets for mTOR signaling-related neurological disorders. ? The Author(s) 2017.11Ysciescopu