Transcriptional landscape of psoriasis identifies the involvement of IL36 and IL36RN

Background In present study we performed whole transcriptome analysis in plaque psoriasis patients and compared lesional skin with non-lesional skin and with the skin from healthy controls. We sequenced total RNA from 12 lesional (LP), 12 non-lesional (NLP) and from 12 normal (C) skin biopsies. Results Compared with previous gene expression profiling studies we had three groups under analysis - LP, NLP and C. Using NLP samples allows to see the transcriptome of visually normal skin from psoriasis patient. In LP skin S100A12, S100A7A, LCE3E, DEFB4A, IL19 were found up regulated. In addition to already these well-described genes, we also found several other genes related to psoriasis. Namely, KLK9, OAS2, OAS3, PLA2G, IL36G, IL36RN were found to be significantly and consistently related to the psoriatic lesions and this finding is supported also by previous studies. The genes up-regulated in the LP samples were related to the innate immunity, IL17 and IL10 networks. In NLP samples innate immunity and IL17 network were activated, but activation of IL10 network was not evident. The transcriptional changes characteristic in the NLP samples can be considered as a molecular signature of “dormant psoriasis”. Conclusions Taken together, our study described the transcriptome profile characteristic for LP and NLP psoriatic skin. RNA profile of the NLP skin is in between the lesional and healthy skin, with its own specific pattern. We found that both LP and NLP have up-regulated IL17 network, whereas LP skin has up regulated IL10 related cytokines (IL19, IL20, IL24). Moreover, IL36G and IL36RN were identified as strong regulators of skin pathology in both LP and NLP skin samples, with stronger influence in LP samples

Identification of an optimal method for extracting RNA from human skin biopsy, using domestic pig as a model system

To evaluate skin tissue gene expression patterns correctly, extracting sufficient quantities of good quality RNA is essential. However, RNA extraction from skin tissue is challenging, as the hyaluronic acid-collagen matrix is extremely difficult to homogenize. Although there are multiple ways to extract RNA from skin, there are no comparative studies that identify the most critical steps, e.g. sample collection, storage and homogenization. We analysed the various steps involved in RNA extraction (i.e. biopsy collection as dry biopsy or into nucleotide stabilizing reagents, different storage conditions, enzymatic digestion, stator-rotor and bead motion-based homogenizing combined with column-based RNA purification). We hypothesised that domestic pig skin is applicable as a model for human skin studies. Altogether twenty different workflows were tested on pig skin and the four most promising workflows were tested on human skin samples. The optimal strategy for extracting human skin RNA was to collect, store and homogenize the sample in RLT lysis buffer from the RNeasy Fibrous Tissue Kit combined with beta-mercaptoethanol. Both stator-rotor and bead motion-based homogenizing were found to result in high quality and quantity of extracted RNA. Our results confirmed that domestic pig skin can be successfully used as a model for human skin RNA studies

Penentuan Waktu Optimum dalam Pembuatan Bioetanol dari Bonggol Pisang Tanduk(Musa Paradisiaca Formatypisa) melalui Fermentasi

Banana tuber contains 76% starch as a source of organic material that can be changed to bioethanol which is an alternative of fuel oil. This study aimed to determine the optimum time of fermentation in the process of producing bioethanol from banana (musa paradisiaca formatypisa) tuber. In this study the fermentation of banana tuber is determined using saccharomyces cereviseae with the variation time of 3, 4, 5, 6, 7, 8 and 10 days. The stages carried out in this study were preliminary or sample preparation, delignification, hydrolysis, fermentation and separation. Bioethanol from the fermented ricestraw was analyzed using alcoholmeter. The content of bioethanol product increased on days 3 to 7 and reach the optimum on the day 7 which was 8.90%, where on the day 8 and 10 decreased the ethanol content

Assessing the impact of interfering organic matter on soil metaproteomic workflow

Funding: Matthias Waibel was funded by the University of Galway College of Science and the Irish Research Council under GOIPG/2016/1215. The James Hutton Institute receives funding support from the Rural and Environment Science and Analytical Services Division of the Scottish Government. Open access funding provided by IReL.Soil organic matter (SOM) is biologically, chemically, and physically complex. As a major store of nutrients within soil, it plays an important role in nutrient provision to plants. An enhanced understanding of SOM utilisation processes could underpin better fertiliser management for plant growth, with reduced environmental losses. Metaproteomics can allow the characterisation of protein profiles and could help gaining insights into SOM microbial decomposition mechanisms. Here, we applied three different extraction methods to two soil types to recover SOM with different characteristics. Specifically, water extractable organic matter, mineral associated organic matter and protein-bound organic matter were targeted with the aim to investigate the metaproteome enriched in those extractions. As a proof-of-concept replicated extracts from one soil were further analysed for peptide identification using liquid chromatography followed by tandem mass spectrometry. We employ a framework for mining mass spectra for both peptide assignment and fragmentation pattern characterisation. Different extracts were found to exhibit contrasting total protein and humic substance content for the two soils investigated. Overall, water extracts displayed the lowest humic substance content (in both soils) and the highest number of peptide identifications (in the soil investigated) with most frequent peptide hits associated with diverse substrate/ligand binding proteins of Proteobacteria and derived taxa. Our framework also highlighted a strong peptidic signal in unassigned and unmatched spectra, information that is currently not captured by the pipelines employed in this study. Taken together, this work points to specific areas for optimisation in chromatography and mass spectrometry to adequately characterise SOM associated metaproteomes.Publisher PDFPeer reviewe

Expression of Class II Cytokine Genes in Children’s Skin

Immune regulation of the skin plays an important role in susceptibility and development of illnesses. The aim of our study was to localise the interleukin (IL)-10 family of cytokines, in children’s skin and to determine possible age-related differences in the expression level. The mRNA expression level of IL10, IL19, IL20, IL22, IL24, IL26, IL28B, IL29 and their receptors IL10RA, IL10RB, IL20RA, IL20RB, IL22RA1, IL22RA2, IL28RA was compared in skin biopsies of children and adults and in childrens’ skin cells by quantitative real-time PCR (qRT-PCR). Immunohistochemistry was performed to confirm the qRT-PCR findings. We found age-related differences in the expression of IL10RB, IL20, IL20RA, IL22RA1, IL22RA2, IL26 and IL28RA genes. Cell type-dependent expression of IL10 family cytokines was apparent in the skin. In addition to previously known differences in systemic immunological response of adults and children, the present results reveal differences in immune profile of adult and juvenile skin

Exploring the psychological rewards of a familiar semirural landscape: connecting to local nature through a mindful approach

This study analyses a 53,000 word diary of a year engaging with nature through over 200 trips to a semi-rural landscape. Thematic analysis revealed two themes; the transition from observer to nature connectedness and the ways in which the natural environment was experienced once a connection was made. These themes are discussed in relation to theories that seek to explain the positive effect of nature and nature connectedness. The findings are important as they suggest that repeated engagement with local semi-rural countryside can lead to a mindful approach and psychological rewards that do not require travel into the wilderness. The work informs further research into outcomes and processes of nature based interventions such as: trip frequency, duration and diary keeping

Nonclassical correlations in damped quantum solitons

Using cumulant expansion in Gaussian approximation, the internal quantum statistics of damped soliton-like pulses in Kerr media are studied numerically, considering both narrow and finite bandwidth spectral pulse components. It is shown that the sub-Poissonian statistics can be enhanced, under certain circumstances, by absorption, which damps out some destructive interferences. Further, it is shown that both the photon-number correlation and the correlation of the photon-number variance between different pulse components can be highly nonclassical even for an absorbing fiber. Optimum frequency windows are determined in order to realize strong nonclassical behavior, which offers novel possibilities of using solitons in optical fibers as a source of nonclassically correlated light beams.Comment: 15 pages, 11 PS figures (color

Cumulant expansion for studying damped quantum solitons

The quantum statistics of damped optical solitons is studied using cumulant-expansion techniques. The effect of absorption is described in terms of ordinary Markovian relaxation theory, by coupling the optical field to a continuum of reservoir modes. After introduction of local bosonic field operators and spatial discretization pseudo-Fokker-Planck equations for multidimensional s-parameterized phase-space functions are derived. These partial differential equations are equivalent to an infinite set of ordinary differential equations for the cumulants of the phase-space functions. Introducing an appropriate truncation condition, the resulting finite set of cumulant evolution equations can be solved numerically. Solutions are presented in Gaussian approximation and the quantum noise is calculated, with special emphasis on squeezing and the recently measured spectral photon-number correlations [Spaelter et al., Phys. Rev. Lett. 81, 786 (1998)].Comment: 17 pages, 13 figures, revtex, psfig, multicols, published in Phys.Rev.

Alternative approach to electromagnetic field quantization in nonlinear and inhomogeneous media

A simple approach is proposed for the quantization of the electromagnetic field in nonlinear and inhomogeneous media. Given the dielectric function and nonlinear susceptibilities, the Hamiltonian of the electromagnetic field is determined completely by this quantization method. From Heisenberg's equations we derive Maxwell's equations for the field operators. When the nonlinearity goes to zero, this quantization method returns to the generalized canonical quantization procedure for linear inhomogeneous media [Phys. Rev. A, 43, 467, 1991]. The explicit Hamiltonians for the second-order and third-order nonlinear quasi-steady-state processes are obtained based on this quantization procedure.Comment: Corrections in references and introductio

Three-dimensional quantization of the electromagnetic field in dispersive and absorbing inhomogeneous dielectrics

A quantization scheme for the phenomenological Maxwell theory of the full electromagnetic field in an inhomogeneous three-dimensional, dispersive and absorbing dielectric medium is developed. The classical Maxwell equations with spatially varying and Kramers-Kronig consistent permittivity are regarded as operator-valued field equations, introducing additional current- and charge-density operator fields in order to take into account the noise associated with the dissipation in the medium. It is shown that the equal-time commutation relations between the fundamental electromagnetic fields $\hat E$ and $\hat B$ and the potentials $\hat A$ and $\hat \phi$ in the Coulomb gauge can be expressed in terms of the Green tensor of the classical problem. From the Green tensors for bulk material and an inhomogeneous medium consisting of two bulk dielectrics with a common planar interface it is explicitly proven that the well-known equal-time commutation relations of QED are preserved