A comparison of local phosphorescence detection and fluid dynamic gauging methods for studying the removal of cohesive fouling layers: Effect of layer roughness

The performance of industrial cleaning in place (CIP) procedures is critically important for food manufacture. CIP has yet to be optimised for many processes, in part since the mechanisms involved in cleaning are not fully understood. Laboratory tests have an important role in guiding industrial trials, and this paper introduces and compares two experimental techniques developed for studying CIP mechanisms: local phosphorescence detection (LPD), and scanning fluid dynamic gauging (sFDG). To illustrate the comparison, each technique is used to investigate the influence of soil topology on the cleaning of pre-gelatinised starch-based layers from 316 stainless steel substrates by aqueous NaOH solutions at ambient temperature. The roughness of the soil surface is varied by incorporating zinc sulphide particles with different particle size distributions (range 1 - 80 μm) into the starch suspensions. The soil roughness increased with the use of larger particles, increasing the 3D arithmetic mean roughness (Sa) of the dry layers (range 0.37 - 3.33 μm). Rough layers were cleaned more readily than those containing small inclusions, with a good correlation between the cleaning rates observed during LPD and FDG measurements. The LPD technique, which is an instrumented CIP test, gives a better indication of the cleaning time, while sFDG measurements provide further insight into the removal mechanisms.NOTICE: this is the author's version of a work that was accepted for publication in Food Bioproducts Processing. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Food Bioproducts Proc., 92, 46-53 DOI http://dx.doi.org/10.1016/j.fbp.2013.07.01

Oct4 differentially regulates chromatin opening and enhancer transcription in pluripotent stem cells

The transcription factor Oct4 is essential for the maintenance and induction of stem cell pluripotency, but its functional roles are not fully understood. Here, we investigate the functions of Oct4 by depleting and subsequently recovering it in mouse embryonic stem cells (ESCs) and conducting a time-resolved multiomics analysis. Oct4 depletion leads to an immediate loss of its binding to enhancers, accompanied by a decrease in mRNA synthesis from its target genes that are part of the transcriptional network that maintains pluripotency. Gradual decrease of Oct4 binding to enhancers does not immediately change the chromatin accessibility but reduces transcription of enhancers. Conversely, partial recovery of Oct4 expression results in a rapid increase in chromatin accessibility, whereas enhancer transcription does not fully recover. These results indicate different concentration-dependent activities of Oct4. Whereas normal ESC levels of Oct4 are required for transcription of pluripotency enhancers, low levels of Oct4 are sufficient to retain chromatin accessibility, likely together with other factors such as Sox2

Natural formation of chloro- and bromoacetone in salt lakes of Western Australia

Western Australia is a semi-/arid region known for saline lakes with a wide range of geochemical parameters (pH 2.5-7.1, Cl- 10-200 g L-1. This study reports on the haloacetones chloro- and bromoacetone in air over 6 salt lake shorelines. Significant emissions of chloroacetone (up to 0.2 µmol m-2 h-1) and bromoacetone (up to 1. 5 µmol m-2 h-1) were detected, and a photochemical box model was employed to evaluate the contribution of their atmospheric formation from the olefinic hydrocarbons propene and methacrolein in the gas phase. The measured concentrations could not explain the photochemical halogenation reaction, indicating a strong hitherto unknown source of haloacetones. Aqueous-phase reactions of haloacetones, investigated in the laboratory using humic acid in concentrated salt solutions, were identified as alternative formation pathway by liquid-phase reactions, acid catalyzed enolization of ketones, and subsequent halogenation. In order to verify this mechanism, we made measurements of the Henry's law constants, rate constants for hydrolysis and nucleophilic exchange with chloride, UV-spectra and quantum yields for the photolysis of bromoacetone and 1,1-dibromoacetone in the aqueous phase. We suggest that heterogeneous processes induced by humic substances in the quasi-liquid layer of the salt crust, particle surfaces and the lake water are the predominating pathways for the formation of the observed haloacetones

Analysis of protein-coding mutations in hiPSCs and their possible role during somatic cell reprogramming

Recent studies indicate that human-induced pluripotent stem cells contain genomic structural variations and point mutations in coding regions. However, these studies have focused on fibroblast-derived human induced pluripotent stem cells, and it is currently unknown whether the use of alternative somatic cell sources with varying reprogramming efficiencies would result in different levels of genetic alterations. Here we characterize the genomic integrity of eight human induced pluripotent stem cell lines derived from five different non-fibroblast somatic cell types. We show that protein-coding mutations are a general feature of the human induced pluripotent stem cell state and are independent of somatic cell source. Furthermore, we analyse a total of 17 point mutations found in human induced pluripotent stem cells and demonstrate that they do not generally facilitate the acquisition of pluripotency and thus are not likely to provide a selective advantage for reprogramming

GAA Deficiency in Pompe Disease Is Alleviated by Exon Inclusion in iPSC-Derived Skeletal Muscle Cells

Pompe disease is a metabolic myopathy caused by deficiency of the acid α-glucosidase (GAA) enzyme and results in progressive wasting of skeletal muscle cells. The c.-32-13T>G (IVS1) GAA variant promotes exon 2 skipping during pre-mRNA splicing and is the most common variant for the childhood/adult disease form. We previously identified antisense oligonucleotides (AONs) that promoted GAA exon 2 inclusion in patient-derived fibroblasts. It was unknown how these AONs would affect GAA splicing in skeletal muscle cells. To test this, we expanded induced pluripotent stem cell (iPSC)-derived myogenic progenitors and differentiated these to multinucleated myotubes. AONs restored splicing in myotubes to a similar extent as in fibroblasts, suggesting that they act by modulating the action of shared splicing regulators. AONs targeted the putative polypyrimidine tract of a cryptic splice acceptor site that was part of a pseudo exon in GAA intron 1. Blocking of the cryptic splice donor of the pseudo exon with AONs likewise promoted GAA exon 2 inclusion. The simultaneous blocking of the cryptic acceptor and cryptic donor sites restored the majority of canonical splicing and alleviated GAA enzyme deficiency. These results highlight the relevance of cryptic splicing in human disease and its potential as therapeutic target for splicing modulation using AONs

A fully automated high-throughput workflow for 3D-based chemical screening in human midbrain organoids

Three-dimensional (3D) culture systems have fueled hopes to bring about the next generation of more physiologically relevant high-throughput screens (HTS). However, current protocols yield either complex but highly heterogeneous aggregates ('organoids') or 3D structures with less physiological relevance ('spheroids'). Here, we present a scalable, HTS-compatible workflow for the automated generation, maintenance, and optical analysis of human midbrain organoids in standard 96-well-plates. The resulting organoids possess a highly homogeneous morphology, size, global gene expression, cellular composition, and structure. They present significant features of the human midbrain and display spontaneous aggregate-wide synchronized neural activity. By automating the entire workflow from generation to analysis, we enhance the intra- and inter-batch reproducibility as demonstrated via RNA sequencing and quantitative whole mount high-content imaging. This allows assessing drug effects at the single-cell level within a complex 3D cell environment in a fully automated HTS workflow

Changing POU dimerization preferences converts Oct6 into a pluripotency inducer

� 2016 The Authors. Published under the terms of the CC BY 4.0 license The transcription factor Oct4 is a core component of molecular cocktails inducing pluripotent stem cells (iPSCs), while other members of the POU family cannot replace Oct4 with comparable efficiency. Rather, group III POU factors such as Oct6 induce neural lineages. Here, we sought to identify molecular features determining the differential DNA-binding and reprogramming activity of Oct4 and Oct6. In enhancers of pluripotency genes, Oct4 cooperates with Sox2 on heterodimeric SoxOct elements. By re-analyzing ChIP-Seq data and performing dimerization assays, we found that Oct6 homodimerizes on palindromic OctOct more cooperatively and more stably than Oct4. Using structural and biochemical analyses, we identified a single amino acid directing binding to the respective DNA elements. A change in this amino acid decreases the ability of Oct4 to generate iPSCs, while the reverse mutation in Oct6 does not augment its reprogramming activity. Yet, with two additional amino acid exchanges, Oct6 acquires the ability to generate iPSCs and maintain pluripotency. Together, we demonstrate that cell type-specific POU factor function is determined by select residues that affect DNA-dependent dimerization.Link_to_subscribed_fulltex

Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells

Generation of human induced pluripotent stem cells (hiPSCs) by the expression of specific transcription factors depends on successful epigenetic reprogramming to a pluripotent state. Although hiPSCs and human embryonic stem cells (hESCs) display a similar epigenome, recent reports demonstrated the persistence of specific epigenetic marks from the somatic cell type of origin and aberrant methylation patterns in hiPSCs. However, it remains unknown whether the use of different somatic cell sources, encompassing variable levels of se- lection pressure during reprogramming, influences the level of epigenetic aberrations in hiPSCs. In this work, we characterized the epigenomic integrity of 17 hiPSC lines derived from six different cell types with varied reprogramming efficiencies. We demonstrate that epigenetic aberrations are a general feature of the hiPSC state and are independent of the somatic cell source. Interestingly, we observe that the reprogramming efficiency of somatic cell lines inversely correlates with the amount of methylation change needed to acquire pluripotency. Additionally, we determine that both shared and line- specific epigenetic aberrations in hiPSCs can directly translate into changes in gene expression in both the pluripotent and differenti- ated states. Significantly, our analysis of different hiPSC lines from multiple cell types of origin allow us to identify a reprogramming- specific epigenetic signature comprised of nine aberrantly methyl- ated genes that is able to segregate hESC and hiPSC lines regardless of the somatic cell source or differentiation state

Associations between preschool attendance and developmental impairments in pre-school children in a six-year retrospective survey

BACKGROUND: Many school-aged children suffer physical and mental impairments which can adversely affect their development and result in significant morbidity. A high proportion of children in western countries attend pre-school, and it is likely that the preschool environment influences the prevalence and severity of these impairments. Currently there is insufficient data available on the prevalence of these impairments and their causal associations. The influence that location of a pre-school and the duration of preschool attendance have on the prevalence of these impairments is not known. METHODS: In a retrospective survey spanning six years (1997–2002) we reviewed the records of 6,230 preschool children who had undergone routine school entry assessments. These children had been assessed utilising a modified manual of the "Bavarian Model" for school entry examinations. This model outlines specific criteria for impairments of motor, cognitive, behavioural and psychosocial functioning. Prevalence rates for physical and behavioural impairments were based on the results of these assessments. The relationship between the prevalence of impairments and the duration of preschool attendance and the location of the preschool attended was estimated utilizing logistic regression models. RESULTS: We found that 20.7% of children met the criteria for at least one type of impairment. Highest prevalence rates (11.5%) were seen for speech impairments and lowest (3.5%) for arithmetic impairments. Boys were disproportionately over represented, with 25.5% meeting the criteria for impairment, compared to 13.0% for girls. Children who had attended preschool for less than one year demonstrated higher rates of impairment (up to 19.1% for difficulties with memory, concentration or perseverance) compared to those who had attended for a longer duration (up to 11.6% for difficulties with pronouncation). Children attending preschool in an urban location had slightly elevated rates of impairment (up to 12.7%), compared to their rural counterparts (up to 11.1%). CONCLUSION: Our results demonstrate that there are high prevalence rates for physical and mental impairments among preschool children. Furthermore, children without preschool experience are a risk group for struggling with educational successes. The associations between the duration of preschool attendance and location of preschool attended and rates of impairment need replication and further exploration. Larger prospective studies are needed to examine if these relationships are causal and may therefore lend themselves to specific intervention strategies